Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr1
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 35726063
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1821929 characters in sequence are not A, C, G, or T
File 8 of 109
Found at i:2616407 original size:36 final size:36
Alignment explanation
Indices: 2616357--2616429 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
2616347 AGACCCAACA
*
2616357 ATCAAGTAGAGTAAGGGGTGTTACATAGGTTGACTT
1 ATCAAGTAGAGTAAGGGGTGTTACATAGGCTGACTT
*
2616393 ATCAAGTAGGGTAAGGGGTGTTACATAGGCTGACTT
1 ATCAAGTAGAGTAAGGGGTGTTACATAGGCTGACTT
2616429 A
1 A
2616430 GGCGAATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.30, C:0.10, G:0.32, T:0.29
Consensus pattern (36 bp):
ATCAAGTAGAGTAAGGGGTGTTACATAGGCTGACTT
Found at i:2619692 original size:19 final size:19
Alignment explanation
Indices: 2619654--2619692 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2619644 AAATAGTGAG
*
2619654 AACTTATTTTCTAAGTATA
1 AACTTATTTTCTAAGAATA
2619673 AACTATATTTTCT-AGAATA
1 AACT-TATTTTCTAAGAATA
2619692 A
1 A
2619693 CAATTTTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (19 bp):
AACTTATTTTCTAAGAATA
Found at i:2622812 original size:17 final size:17
Alignment explanation
Indices: 2622790--2622822 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2622780 TACTTAAATT
2622790 AATTATATAAA-ATAAAA
1 AATTAT-TAAATATAAAA
2622807 AATTATTAAATATAAA
1 AATTATTAAATATAAA
2622823 CATATCGACG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATTATTAAATATAAAA
Found at i:2626329 original size:34 final size:34
Alignment explanation
Indices: 2626286--2626354 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
2626276 TTCAGTTCAT
2626286 TAACTTCTATTATCAACATTAGCAGGTAGAATTC
1 TAACTTCTATTATCAACATTAGCAGGTAGAATTC
2626320 TAACTTCTATTATCAACATTAGCAGGTAGAATTC
1 TAACTTCTATTATCAACATTAGCAGGTAGAATTC
2626354 T
1 T
2626355 TACATGCTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (34 bp):
TAACTTCTATTATCAACATTAGCAGGTAGAATTC
Found at i:2638657 original size:2 final size:2
Alignment explanation
Indices: 2638650--2638687 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2638640 TTATATGTAC
*
2638650 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2638688 TATTTTTATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:2639068 original size:107 final size:106
Alignment explanation
Indices: 2638786--2639145 Score: 544
Period size: 106 Copynumber: 3.4 Consensus size: 106
2638776 ATTTTTTTAC
* *
2638786 TGGGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCATTCTAAAATTTCAAAGTAAGACAAT
1 TGGGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTCTAAAATTTCAAAGTAAGGCAAT
* * *
2638851 ATTTTGAGTTT-GAAAATTCGAGAAAACGTGTCCTAATGTGC
66 ATTTTGCGTTTAG-AAATTCGAGAAAACGTGCCCTAATGTGT
* * * *
2638892 TGGGTTTCAATTTCTCATTCGACCAAATAGCCAAATATCCTTCTAAAATTTCAAAATAAAGCAAT
1 TGGGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTCTAAAATTTCAAAGTAAGGCAAT
2638957 ATTTTGCGTTTAGAAATTCGAGAAAACGTGCCCTAATGTGT
66 ATTTTGCGTTTAGAAATTCGAGAAAACGTGCCCTAATGTGT
* * *
2638998 TGGGTTTCGATTTTTTCGTTCAACCAAATAGCCAAATATCCTAT-TAAAATTTCAAAGTAAGGTA
1 TGGGTTTCGA-TTTCTCGTTCGACCAAATAGCCAAATATCCT-TCTAAAATTTCAAAGTAAGGCA
*
2639062 ATATTTTGCGTTTAGAAATTCGAGAAAACGTGCCCTAACGTGT
64 ATATTTTGCGTTTAGAAATTCGAGAAAACGTGCCCTAATGTGT
* *
2639105 TGGGTTTCGATTTCTCGTTTGACCAAATAACCAAATATCCT
1 TGGGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCT
2639146 CTTAAATCTC
Statistics
Matches: 230, Mismatches: 21, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
106 131 0.57
107 98 0.43
108 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (106 bp):
TGGGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTCTAAAATTTCAAAGTAAGGCAAT
ATTTTGCGTTTAGAAATTCGAGAAAACGTGCCCTAATGTGT
Found at i:2643791 original size:20 final size:20
Alignment explanation
Indices: 2643740--2643796 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
2643730 AATACTTTAA
*
2643740 AAAAGACGAAAAAAAGAAAAG
1 AAAA-ACGAAAAAGAGAAAAG
*
2643761 AAAAACAAAAAAGAGAAAAG
1 AAAAACGAAAAAGAGAAAAG
* *
2643781 AAAAAGGAAAATGAGA
1 AAAAACGAAAAAGAGA
2643797 GGCCAATGTG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 27 0.87
21 4 0.13
ACGTcount: A:0.75, C:0.04, G:0.19, T:0.02
Consensus pattern (20 bp):
AAAAACGAAAAAGAGAAAAG
Found at i:2644384 original size:106 final size:106
Alignment explanation
Indices: 2644057--2644383 Score: 501
Period size: 106 Copynumber: 3.1 Consensus size: 106
2644047 GGGGTACTTG
* * *
2644057 TTTTCATCTTATTCATTTCGGATCTTAGCAAAATTTTCTATTTTGATTAATTTATTCATTTCAAG
1 TTTTCATCTTATTCAGTTC-G-TCTTAGCAAAATTTGCTATTTTGATTAATTTATTCATTTCGAG
2644122 CTTTGCTCTCAATAAAATTCCATCTTGTCCATTGTGATAATCT
64 CTTTGCTCTCAATAAAATTCCATCTTGTCCATTGTGATAATCT
* * *
2644165 TTTTCATCTTATTCAGTTCATCATAGCAAAATTTGCTATTTTGTTTAATTTATTCATTTCGAGCT
1 TTTTCATCTTATTCAGTTCGTCTTAGCAAAATTTGCTATTTTGATTAATTTATTCATTTCGAGCT
* *
2644230 TTGCTCTTAATAAAATTCCATGTTGTCCATTGTGATAATCT
66 TTGCTCTCAATAAAATTCCATCTTGTCCATTGTGATAATCT
* *
2644271 TTTTCATTTTATTCAGTTCGTCTTAGCAAAATTTGCTATTTTGGTTAATTTATTCATTTCGAGCT
1 TTTTCATCTTATTCAGTTCGTCTTAGCAAAATTTGCTATTTTGATTAATTTATTCATTTCGAGCT
** ** *
2644336 TTATTCTCAATAAAATTTTATCTTGTCCATTGTGATAATAT
66 TTGCTCTCAATAAAATTCCATCTTGTCCATTGTGATAATCT
2644377 TTTTCAT
1 TTTTCAT
2644384 TGAAATAACT
Statistics
Matches: 200, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
106 182 0.91
108 18 0.09
ACGTcount: A:0.25, C:0.16, G:0.09, T:0.50
Consensus pattern (106 bp):
TTTTCATCTTATTCAGTTCGTCTTAGCAAAATTTGCTATTTTGATTAATTTATTCATTTCGAGCT
TTGCTCTCAATAAAATTCCATCTTGTCCATTGTGATAATCT
Found at i:2644873 original size:24 final size:24
Alignment explanation
Indices: 2644841--2644898 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
2644831 ATGTCCCAAA
*
2644841 ATTATAGTGGA-TTGAATCTTGAAG
1 ATTACAGTGGATTTGAAT-TTGAAG
*
2644865 ATTACAGTGGATTTGACTTTGAAG
1 ATTACAGTGGATTTGAATTTGAAG
2644889 ATTACAGTGG
1 ATTACAGTGG
2644899 GGGCAATCCG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 26 0.84
25 5 0.16
ACGTcount: A:0.31, C:0.07, G:0.26, T:0.36
Consensus pattern (24 bp):
ATTACAGTGGATTTGAATTTGAAG
Found at i:2645437 original size:132 final size:132
Alignment explanation
Indices: 2645257--2645928 Score: 983
Period size: 132 Copynumber: 5.1 Consensus size: 132
2645247 GCACCAGCCT
* * * * *
2645257 TATCTCCTTGAGTAGCAATGGAGTAGGTCGAAGATTGTAGATCTTGTCTCCTTAAGCAGTAGTGG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTCGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGG
* *
2645322 AGCAGATCGAAGACAGAGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCATCAGT
66 AGCAGATCGAAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCATCAGT
2645387 CC
131 CC
* *
2645389 TATCTCCCAGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTCGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGG
* *
2645454 AGCAAATTGAAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCATCAG-
66 AGCAGATCGAAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCATCAGT
2645518 CC
131 CC
* *
2645520 TTATCTTCTTGAGCAGCAGTGGAGTAGGTCGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTG
1 -TATCTCCCTGAGCAGCAGTGGAGTAGGTCGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTG
* * * * *
2645585 GAGCAAATCGAAGACGGTGGATCTTATCTTCCCAATGTAGTAGGGAAACAGATTTAAGCCACCAG
65 GAGCAGATCGAAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCATCAG
2645650 -CC
130 TCC
* *
2645652 TTATCTCTCTGAGCAGTAGTGGAGTAGGTCGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTG
1 -TATCTCCCTGAGCAGCAGTGGAGTAGGTCGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTG
* *
2645717 GAGCAGATCGAAGACGGTGAATCTTATCTTCTCAAGGTAGTAGGGAAGCTA-ATTTAAGCCATTA
65 GAGCAGATCGAAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGC-AGATTTAAGCCATCA
2645781 GTCC
129 GTCC
* * * *
2645785 TATCCCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCCTATCTCCCTAAGCAGTAGTGG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTCGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGG
* ** * * * *
2645850 AACAGATCGAAGACGACGAATCTTATCTTTCCAAGGTAGTAGGGAAACATATTTAAGCCA-CAAA
66 AGCAGATCGAAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCATC-AG
2645914 TCC
130 TCC
2645917 TATCTCCCTGAG
1 TATCTCCCTGAG
2645929 ATTGCAGTAG
Statistics
Matches: 489, Mismatches: 46, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
131 3 0.01
132 483 0.99
133 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (132 bp):
TATCTCCCTGAGCAGCAGTGGAGTAGGTCGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGG
AGCAGATCGAAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCATCAGT
CC
Found at i:2645596 original size:44 final size:44
Alignment explanation
Indices: 2645275--2645863 Score: 196
Period size: 44 Copynumber: 13.4 Consensus size: 44
2645265 TGAGTAGCAA
* * * * * *
2645275 TGGAGTAGGTCGAAGATTGTAGATCTTGTCTCCTTAAGCAGTAG
1 TGGAGCAGATCGAAGACTGTAGATCCTATCTCCCTAAGCAGTAG
* * *
2645319 TGGAGCAGATCGAAGACAG-AGAATCTTATCTTCCC-AAGGTAGTAG
1 TGGAGCAGATCGAAGACTGTAG-ATCCTATC-TCCCTAA-GCAGTAG
** * * *
2645364 -GGAAGCAGATTTAAGCCAT-CAG-TCCTATCTCCC-AGAGCAGCAG
1 TGG-AGCAGATCGAAGAC-TGTAGATCCTATCTCCCTA-AGCAGTAG
* * * * *
2645407 TGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAG
1 TGGAGCAGATCGAAGACTGTAGATCCTATCTCCCTAAGCAGTAG
* * * * *
2645451 TGGAGCAAATTGAAGACGGT-GAATCTTATCTTCCC-AAGGTAGTAG
1 TGGAGCAGATCGAAGACTGTAG-ATCCTATC-TCCCTAA-GCAGTAG
** * * * * * *
2645496 -GGAAGCAGATTTAAGCCAT-CAG--CCTTATCTTCTTGAGCAGCAG
1 TGG-AGCAGATCGAAGAC-TGTAGATCC-TATCTCCCTAAGCAGTAG
* * * *
2645539 TGGAGTAGGTCGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAG
1 TGGAGCAGATCGAAGACTGTAGATCCTATCTCCCTAAGCAGTAG
* * * * *
2645583 TGGAGCAAATCGAAGACGGTGGATCTTATCTTCCC-AATGTAGTAG
1 TGGAGCAGATCGAAGACTGTAGATCCTATC-TCCCTAA-GCAGTAG
* ** * *** * *
2645628 -GGAAACAGATTTAAGCCACCAG--CCTTATCTCTCTGAGCAGTAG
1 TGG-AGCAGATCGAAGACTGTAGATCC-TATCTCCCTAAGCAGTAG
* * * *
2645671 TGGAGTAGGTCGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAG
1 TGGAGCAGATCGAAGACTGTAGATCCTATCTCCCTAAGCAGTAG
* * * *
2645715 TGGAGCAGATCGAAGACGGT-GAATCTTATCT-TCTCAAGGTAGTAG
1 TGGAGCAGATCGAAGACTGTAG-ATCCTATCTCCCT-AA-GCAGTAG
** * * * *
2645760 -GGAAGCTA-ATTTAAGCCAT-TAG-TCCTATCCCCCTGAGCAGCAG
1 TGG-AGC-AGATCGAAGAC-TGTAGATCCTATCTCCCTAAGCAGTAG
* * * * *
2645803 TGGAGTAGGTTGAAGATTGCAGATCCTATCTCCCTAAGCAGTAG
1 TGGAGCAGATCGAAGACTGTAGATCCTATCTCCCTAAGCAGTAG
*
2645847 TGGAACAGATCGAAGAC
1 TGGAGCAGATCGAAGAC
2645864 GACGAATCTT
Statistics
Matches: 382, Mismatches: 120, Indels: 86
0.65 0.20 0.15
Matches are distributed among these distances:
42 4 0.01
43 78 0.20
44 211 0.55
45 84 0.22
46 5 0.01
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (44 bp):
TGGAGCAGATCGAAGACTGTAGATCCTATCTCCCTAAGCAGTAG
Found at i:2646013 original size:41 final size:42
Alignment explanation
Indices: 2645912--2646146 Score: 138
Period size: 44 Copynumber: 5.5 Consensus size: 42
2645902 TTAAGCCACA
* * * *
2645912 AATCCTATCTCCCTG-AGATTGCAGTAGA-ACGGATTAAAACCAC
1 AATCTTATCTCCCTGAAG-TTGCAGTAGAGACAGA-TAGAATC-C
* * *
2645955 AGATCTTATCTCTCTGAAGTTGCAGTAGAG-CAGATCGCATCC
1 A-ATCTTATCTCCCTGAAGTTGCAGTAGAGACAGATAGAATCC
*
2645997 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGA-AGAAGCC
1 AATCTTATCTCCCTGAAGTTGCAGT--AG-AGACAGATAGAATCC
* ** * *** * * *
2646041 AATCCTATCTCCACAAAAGTTACAGTAGAGTGGGTTAAAACTAC
1 AATCTTATCTCC-CTGAAGTTGCAGTAGAGACAGATAGAA-TCC
* * * *
2646085 AGATATTATCTCTCTGAAGTTGCAGTAGAG-CAGATCGCATCC
1 A-ATCTTATCTCCCTGAAGTTGCAGTAGAGACAGATAGAATCC
*
2646127 AGTCTTATCTCCCTGAAGTT
1 AATCTTATCTCCCTGAAGTT
2646147 ATAGTGGAGC
Statistics
Matches: 143, Mismatches: 38, Indels: 24
0.70 0.19 0.12
Matches are distributed among these distances:
41 39 0.27
42 8 0.06
43 14 0.10
44 58 0.41
45 24 0.17
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (42 bp):
AATCTTATCTCCCTGAAGTTGCAGTAGAGACAGATAGAATCC
Found at i:2646175 original size:130 final size:129
Alignment explanation
Indices: 2645936--2646252 Score: 395
Period size: 130 Copynumber: 2.4 Consensus size: 129
2645926 GAGATTGCAG
*
2645936 TAGAACGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAATC
1 TAGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAATC
* * *
2646001 TTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAGCCAATCCTATCTCCACAAAAGTTACAG
66 TTATCTCCCTGAAGTTACAGTGGAGCAAACAGAAGAAGCCAATCCTATCT-CACAAAAGTTACAA
* * * * *
2646066 TAGAGTGGGTTAAAACTACAGATATTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTC
1 TAGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAATC
* ** * ** ** *
2646131 TTATCTCCCTGAAGTTATAGTGGAGCAAATTGAAGTTA-TTAATCCTATCTCACTGAAGTTGCAA
66 TTATCTCCCTGAAGTTACAGTGGAGCAAACAGAAG-AAGCCAATCCTATCTCACAAAAGTTACAA
* * * *
2646195 TGGAGCGGATTAAAACGA-TGAATCTTATCTCTTTGAAGTTGCAGTAGAGCAGATCGCA
1 TAGAGCGGATTAAAACCACAG-ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCA
2646253 CCATAATAAG
Statistics
Matches: 160, Mismatches: 25, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
128 1 0.01
129 59 0.37
130 99 0.62
131 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (129 bp):
TAGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAATC
TTATCTCCCTGAAGTTACAGTGGAGCAAACAGAAGAAGCCAATCCTATCTCACAAAAGTTACAA
Found at i:2646373 original size:44 final size:44
Alignment explanation
Indices: 2645957--2646425 Score: 264
Period size: 44 Copynumber: 10.8 Consensus size: 44
2645947 AAAACCACAG
* * * *
2645957 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCG--CAT-CCA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACCA
**
2645998 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGA-AGCCA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-CCA
* ** * * ** * *
2646042 ATCCTATCTCCACAAAAGTTACAGTAGAGTGGGTT-AAAACTA-CA
1 ATCTTATCTCC-CTGAAGTTGCAGTGGAGCAGATTGAAGA-TACCA
* * * * *
2646086 GATATTATCTCTCTGAAGTTGCAGTAGAGCAGATCG--CAT-CCA
1 -ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACCA
* ** * * **
2646128 GTCTTATCTCCCTGAAGTTATAGTGGAGCAAATTGAAGTTATTA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACCA
* * * * * *
2646172 ATCCTATCTCACTGAAGTTGCAATGGAGCGGATTAAAACGAT--GA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-GAA-GATACCA
** * * ** **
2646216 ATCTTATCTCTTTGAAGTTGCAGTAGAGCAGATCGCACCATAATA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTG-AAGATACCA
* * *
2646261 AGTCTTATCT-CCTTAGAGTTGAAGTGGAGCAGACTGAAGATA--A
1 A-TCTTATCTCCCTGA-AGTTGCAGTGGAGCAGATTGAAGATACCA
** * * *
2646304 GCCTTATCTCCCTAAAGTTGTAGTGGAGCAGGTTGAAGATACCA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACCA
* * **
2646348 ATCTTATCTCCCTGAAGTTGCAGTGGAGCTGATTGAAGCTATTA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACCA
* *
2646392 ATCTTGTCTCCCTGAAGTTGCAGTGGAGCGGATT
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT
2646426 AAAACGATAA
Statistics
Matches: 318, Mismatches: 87, Indels: 43
0.71 0.19 0.10
Matches are distributed among these distances:
41 58 0.18
42 33 0.10
43 10 0.03
44 158 0.50
45 32 0.10
46 27 0.08
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACCA
Found at i:2646451 original size:44 final size:44
Alignment explanation
Indices: 2646171--2646455 Score: 147
Period size: 44 Copynumber: 6.5 Consensus size: 44
2646161 TGAAGTTATT
* * *
2646171 AATCCTATCTCACTGAAGTTGCAATGGAGCGGATTAAAACGATG
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACGATA
* ** * * *** *
2646215 AATCTTATCTCTTTGAAGTTGCAGTAGAGCAGA-TCGCACCATAA
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACGAT-A
* * * * * *
2646259 TAAGTCTTATCT-CCTTAGAGTTGAAGTGGAGCAGACT-GAA-GAT-
1 -AA-TCCTATCTCCCTGA-AGTTGCAGTGGAGCGGATTAAAACGATA
* * * *
2646302 AAGCCTTATCTCCCTAAAGTTGTAGTGGAGCAGG-TT-GAA-GATA
1 AATCC-TATCTCCCTGAAGTTGCAGTGGAGC-GGATTAAAACGATA
* * * * * *
2646345 CCAATCTTATCTCCCTGAAGTTGCAGTGGAGCTGATTGAAGCTATT
1 --AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACGATA
* *
2646391 AATCTTGTCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACGATA
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACGATA
*
2646435 AATCCTATAC-CTCTGAAGTTG
1 AATCCTAT-CTCCCTGAAGTTG
2646456 TAGTAAGTTG
Statistics
Matches: 184, Mismatches: 42, Indels: 30
0.72 0.16 0.12
Matches are distributed among these distances:
41 1 0.01
42 27 0.15
43 11 0.06
44 106 0.58
45 11 0.06
46 27 0.15
47 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (44 bp):
AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACGATA
Found at i:2648390 original size:20 final size:21
Alignment explanation
Indices: 2648367--2648411 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
2648357 TTTCTCATAT
2648367 TATTT-TTGTTTACATTAT-CA
1 TATTTATTG-TTACATTATGCA
*
2648387 TATTTATTGTTCCATTATGCA
1 TATTTATTGTTACATTATGCA
2648408 TATT
1 TATT
2648412 AACATCATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.24, C:0.11, G:0.07, T:0.58
Consensus pattern (21 bp):
TATTTATTGTTACATTATGCA
Found at i:2648672 original size:107 final size:104
Alignment explanation
Indices: 2648452--2648863 Score: 581
Period size: 107 Copynumber: 3.9 Consensus size: 104
2648442 CTAAATAAGA
* *
2648452 CAATATTTTGCGTTTGGAAATTCGAGAAAATGTGCCCTAATGTGCTGGGTTTCGATTTCTCGTTC
1 CAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCAATTTCTCGTTC
* *
2648517 GACCAAATAGCCAAATGTCCTTTTAAAATTTCAAAGGAAGG
66 GACCAAATAGCCAAATATCC-TTTAAAATTTCAAA-GTAGG
* *
2648558 CAATATTTTGCGTTTGGAAATTCGAGAAAACGTGTCCTAATGTGCTGGGTTTCAATTTTTTCGTT
1 CAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCAA-TTTCTCGTT
2648623 CGACCAAATAGCCAAATATCCTTCTAAAATTTCAAAGTAGG
65 CGACCAAATAGCCAAATATCCTT-TAAAATTTCAAAGTAGG
* * * *
2648664 ACAATATTTTGCTTTTGGAAATTCGAGAAAATGTGCCCTAATGTGCTGGGTTTCGATTTTTTCGT
1 -CAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTC-AATTTCTCGT
* *
2648729 TCAACCAAATAGCCAAATATCCTATTAAAAATTCAAAGTAAGG
64 TCGACCAAATAGCCAAATATCCT-TTAAAATTTCAAAGT-AGG
* * * * *
2648772 CAATATTTTGCGTTTGGAAATTCGAGAAAACGTACCCTAACGTGCTGTGTTTCAATTTCTCATTT
1 CAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCAATTTCTCGTTC
*
2648837 GACTAAATAGCCAAATATCCTCTTAAA
66 GACCAAATAGCCAAATATCCT-TTAAA
2648864 TCTCAATCCA
Statistics
Matches: 276, Mismatches: 24, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
106 90 0.33
107 181 0.66
108 5 0.02
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (104 bp):
CAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCAATTTCTCGTTC
GACCAAATAGCCAAATATCCTTTAAAATTTCAAAGTAGG
Found at i:2648826 original size:214 final size:212
Alignment explanation
Indices: 2648450--2648857 Score: 663
Period size: 214 Copynumber: 1.9 Consensus size: 212
2648440 TTCTAAATAA
2648450 GACAATATTTTGCGTTTGGAAATTCGAGAAAATGTGCCCTAATGTGCTGGGTTTCGATTTCTCGT
1 GACAATATTTTGCGTTTGGAAATTCGAGAAAATGTGCCCTAATGTGCTGGGTTTCGATTTCTCGT
* * * *
2648515 TCGACCAAATAGCCAAATGTCCTTTTAAAATTTCAAAGGAAGGCAATATTTTGCGTTTGGAAATT
66 TCAACCAAATAGCCAAATATCCTATTAAAAATTCAAAGGAAGGCAATATTTTGCGTTTGGAAATT
** * * *
2648580 CGAGAAAACGTGTCCTAATGTGCTGGGTTTCAATTTTTTCGTTCGACCAAATAGCCAAATATCCT
131 CGAGAAAACGTACCCTAACGTGCTGGGTTTCAA-TTTCTCATTCGACCAAATAGCCAAATATCCT
2648645 TCTAAAATTTCAAAGTAG
195 TCTAAAATTTCAAAGTAG
* *
2648663 GACAATATTTTGCTTTTGGAAATTCGAGAAAATGTGCCCTAATGTGCTGGGTTTCGATTTTTTCG
1 GACAATATTTTGCGTTTGGAAATTCGAGAAAATGTGCCCTAATGTGCTGGGTTTCGA-TTTCTCG
*
2648728 TTCAACCAAATAGCCAAATATCCTATTAAAAATTCAAAGTAAGGCAATATTTTGCGTTTGGAAAT
65 TTCAACCAAATAGCCAAATATCCTATTAAAAATTCAAAGGAAGGCAATATTTTGCGTTTGGAAAT
* * *
2648793 TCGAGAAAACGTACCCTAACGTGCTGTGTTTCAATTTCTCATTTGACTAAATAGCCAAATATCCT
130 TCGAGAAAACGTACCCTAACGTGCTGGGTTTCAATTTCTCATTCGACCAAATAGCCAAATATCCT
2648858 CTTAAATCTC
Statistics
Matches: 179, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
213 83 0.46
214 96 0.54
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (212 bp):
GACAATATTTTGCGTTTGGAAATTCGAGAAAATGTGCCCTAATGTGCTGGGTTTCGATTTCTCGT
TCAACCAAATAGCCAAATATCCTATTAAAAATTCAAAGGAAGGCAATATTTTGCGTTTGGAAATT
CGAGAAAACGTACCCTAACGTGCTGGGTTTCAATTTCTCATTCGACCAAATAGCCAAATATCCTT
CTAAAATTTCAAAGTAG
Found at i:2655618 original size:18 final size:19
Alignment explanation
Indices: 2655592--2655629 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
2655582 AATGTGTCCT
*
2655592 AAATTACATAAT-ATATAA
1 AAATAACATAATAATATAA
2655610 AAATAACATAATAATATAA
1 AAATAACATAATAATATAA
2655629 A
1 A
2655630 GTATTATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (19 bp):
AAATAACATAATAATATAA
Found at i:2656682 original size:23 final size:23
Alignment explanation
Indices: 2656655--2656710 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
2656645 GTTCAATTCA
*
2656655 TTTATTTATAT-T-ATAAATGCTG
1 TTTATTTATATCTAATAAAT-ATG
2656677 TATTATTTTATATCTAATAAATATG
1 T-TTA-TTTATATCTAATAAATATG
2656702 TTTATTTAT
1 TTTATTTAT
2656711 GATTCTCTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 1 0.03
23 8 0.28
24 10 0.34
25 4 0.14
26 6 0.21
ACGTcount: A:0.34, C:0.04, G:0.05, T:0.57
Consensus pattern (23 bp):
TTTATTTATATCTAATAAATATG
Found at i:2661566 original size:6 final size:6
Alignment explanation
Indices: 2661557--2661581 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2661547 GAGTTGGGCA
2661557 TGAGCT TGAGCT TGAGCT TGAGCT T
1 TGAGCT TGAGCT TGAGCT TGAGCT T
2661582 TCGACTGAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.32, T:0.36
Consensus pattern (6 bp):
TGAGCT
Found at i:2662250 original size:2 final size:2
Alignment explanation
Indices: 2662240--2662270 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2662230 AGAGAGTTCG
2662240 TC TC T- TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2662271 CCCCAATTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2662637 original size:31 final size:31
Alignment explanation
Indices: 2662599--2662657 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2662589 GTCATTGAGC
* *
2662599 TATTCAAAATTTTTCATTTAAGTTACTAATT
1 TATTCAAAAGTTTTCATTTAAGTCACTAATT
2662630 TATTCAAAAGTTTTCATTTAAGTCACTA
1 TATTCAAAAGTTTTCATTTAAGTCACTA
2662658 GGTTGTCAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.47
Consensus pattern (31 bp):
TATTCAAAAGTTTTCATTTAAGTCACTAATT
Found at i:2665564 original size:22 final size:22
Alignment explanation
Indices: 2665513--2665566 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
2665503 TATTTTTAAA
2665513 ATTTTAAT-TTAATTATAAAAT
1 ATTTTAATATTAATTATAAAAT
* *
2665534 ATATAAATATTAATTA-AAAAT
1 ATTTTAATATTAATTATAAAAT
2665555 ATTTTTAATATT
1 A-TTTTAATATT
2665567 TTGTTATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTTTAATATTAATTATAAAAT
Found at i:2669683 original size:26 final size:27
Alignment explanation
Indices: 2669642--2669697 Score: 96
Period size: 26 Copynumber: 2.1 Consensus size: 27
2669632 CTTTATAATA
*
2669642 TATTTTTTTTAGTTTTTAAATTTTTTT
1 TATTTTTGTTAGTTTTTAAATTTTTTT
2669669 TATTTTTGTTA-TTTTTAAATTTTTTT
1 TATTTTTGTTAGTTTTTAAATTTTTTT
2669695 TAT
1 TAT
2669698 GATTTTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 18 0.64
27 10 0.36
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.77
Consensus pattern (27 bp):
TATTTTTGTTAGTTTTTAAATTTTTTT
Found at i:2669684 original size:18 final size:18
Alignment explanation
Indices: 2669640--2669675 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2669630 CCCTTTATAA
2669640 TATATTTTTTTTAGTTTT
1 TATATTTTTTTTAGTTTT
*
2669658 TAAATTTTTTTTA-TTTT
1 TATATTTTTTTTAGTTTT
2669675 T
1 T
2669676 GTTATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (18 bp):
TATATTTTTTTTAGTTTT
Found at i:2669690 original size:17 final size:18
Alignment explanation
Indices: 2669670--2669711 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
2669660 AATTTTTTTT
2669670 ATTTTTGTTAT-TTTTAA
1 ATTTTTGTTATATTTTAA
* *
2669687 ATTTTTTTTATGATTTTAT
1 ATTTTTGTTAT-ATTTTAA
2669706 ATTTTT
1 ATTTTT
2669712 TGAGATTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 10 0.48
19 11 0.52
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (18 bp):
ATTTTTGTTATATTTTAA
Found at i:2669710 original size:26 final size:26
Alignment explanation
Indices: 2669654--2669711 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
2669644 TTTTTTTTAG
**
2669654 TTTTTAAATTTTTTTTATTTTTGTTA
1 TTTTTAAATTTTTTTTATGATTGTTA
*
2669680 TTTTTAAATTTTTTTTATGATTTTATA
1 TTTTTAAATTTTTTTTATGATTGT-TA
2669707 TTTTT
1 TTTTT
2669712 TGAGATTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 21 0.75
27 7 0.25
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (26 bp):
TTTTTAAATTTTTTTTATGATTGTTA
Found at i:2671157 original size:29 final size:28
Alignment explanation
Indices: 2671117--2671191 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 28
2671107 TTCTAGATAT
* *
2671117 ATTATTTAGAATTTTTTAAAAAACTATATA
1 ATTATTTTGAATTTTTTAAAAAA-TA-AAA
2671147 ATT-TTTTGAATTTTTATAAAAAATAAAA
1 ATTATTTTGAATTTTT-TAAAAAATAAAA
2671175 ATTATTTTGAATTTTTT
1 ATTATTTTGAATTTTTT
2671192 TTGTAAGCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
28 6 0.15
29 25 0.61
30 10 0.24
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (28 bp):
ATTATTTTGAATTTTTTAAAAAATAAAA
Found at i:2673539 original size:16 final size:17
Alignment explanation
Indices: 2673520--2673563 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
2673510 TTTTTTTACT
*
2673520 TTGGGCCACTGCTGG-G
1 TTGGGCAACTGCTGGTG
*
2673536 TTGGGCAACTGTTGGTG
1 TTGGGCAACTGCTGGTG
*
2673553 TTGGGCTACTG
1 TTGGGCAACTG
2673564 TTGGACAGGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.09, C:0.18, G:0.41, T:0.32
Consensus pattern (17 bp):
TTGGGCAACTGCTGGTG
Found at i:2673557 original size:17 final size:16
Alignment explanation
Indices: 2673520--2673567 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
2673510 TTTTTTTACT
* *
2673520 TTGGGCCACTGCTGGG
1 TTGGGCAACTGTTGGG
2673536 TTGGGCAACTGTTGGTG
1 TTGGGCAACTGTTGG-G
*
2673553 TTGGGCTACTGTTGG
1 TTGGGCAACTGTTGG
2673568 ACAGGCCTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 13 0.46
17 15 0.54
ACGTcount: A:0.08, C:0.17, G:0.42, T:0.33
Consensus pattern (16 bp):
TTGGGCAACTGTTGGG
Found at i:2673950 original size:25 final size:23
Alignment explanation
Indices: 2673922--2673973 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
2673912 TCGTTTCTCT
2673922 TTTTCTC-TCCTCTCTTCTTTTTTTC
1 TTTTCTCAT-CTCTC-T-TTTTTTTC
*
2673947 TTTTCTCATTTCTCTTTTTTTTC
1 TTTTCTCATCTCTCTTTTTTTTC
2673970 TTTT
1 TTTT
2673974 TATTTATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 12 0.48
24 1 0.04
25 11 0.44
26 1 0.04
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTTCTCATCTCTCTTTTTTTTC
Found at i:2673959 original size:32 final size:32
Alignment explanation
Indices: 2673895--2673961 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
2673885 TTTCCTCTCT
*
2673895 TCTCCTCTCTTCATTCTTCGTTTCTCTTTTTC
1 TCTCCTCTCTTCATTCTTCGTTTCTCTATTTC
* * *
2673927 TCTCCTCTCTTCTTTTTTTCTTTTCTC-ATTTC
1 TCTCCTCTCTTC-ATTCTTCGTTTCTCTATTTC
2673959 TCT
1 TCT
2673962 TTTTTTTCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 19 0.63
33 11 0.37
ACGTcount: A:0.03, C:0.33, G:0.01, T:0.63
Consensus pattern (32 bp):
TCTCCTCTCTTCATTCTTCGTTTCTCTATTTC
Found at i:2674583 original size:28 final size:29
Alignment explanation
Indices: 2674514--2674585 Score: 101
Period size: 30 Copynumber: 2.5 Consensus size: 29
2674504 AAAACTCCCA
2674514 GGGCTAAAATGTAATTTTAAAAAAAGTGAG
1 GGGCTAAAATGTAATTTTAAAAAAAGT-AG
* *
2674544 GGGCTAAAATGTAATTTTAGAAATAGT-G
1 GGGCTAAAATGTAATTTTAAAAAAAGTAG
*
2674572 GGGCCAAAATGTAA
1 GGGCTAAAATGTAA
2674586 ATTGTATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
28 14 0.36
30 25 0.64
ACGTcount: A:0.43, C:0.06, G:0.25, T:0.26
Consensus pattern (29 bp):
GGGCTAAAATGTAATTTTAAAAAAAGTAG
Found at i:2674637 original size:14 final size:14
Alignment explanation
Indices: 2674620--2674650 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2674610 AATTTTCCTT
2674620 TTTTCTTATTATTA
1 TTTTCTTATTATTA
2674634 TTTTCTTATTATTA
1 TTTTCTTATTATTA
2674648 TTT
1 TTT
2674651 AAAAATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTCTTATTATTA
Found at i:2676554 original size:140 final size:140
Alignment explanation
Indices: 2676302--2676586 Score: 516
Period size: 140 Copynumber: 2.0 Consensus size: 140
2676292 TGGCCAAGCC
*
2676302 GTGTGACTCACACGGCCAATAGACACACCTGTGTCTTAGGTCGTGTTGGTATTCAAAATAAGAGC
1 GTGTGACTCACACGGCCAAGAGACACACCTGTGTCTTAGGTCGTGTTGGTATTCAAAATAAGAGC
*
2676367 ACATGGCCGTGTCCCAGCCCGTGTAACTCACTGACTTGGGTCACAAGGCCAAACCACACGCCCGT
66 ACACGGCCGTGTCCCAGCCCGTGTAACTCACTGACTTGGGTCACAAGGCCAAACCACACGCCCGT
2676432 GTGCCAGGCA
131 GTGCCAGGCA
* *
2676442 GTGTGACTCACACGGCCAAGAGACACACCTGTGTCTTAGGTCGTGTTGGTATTCAAAATAGGATC
1 GTGTGACTCACACGGCCAAGAGACACACCTGTGTCTTAGGTCGTGTTGGTATTCAAAATAAGAGC
*
2676507 ACACGGTCGTGTCCCAGCCCGTGTAACTCACTGACTTGGGTCACAAGGCCAAACCACACGCCCGT
66 ACACGGCCGTGTCCCAGCCCGTGTAACTCACTGACTTGGGTCACAAGGCCAAACCACACGCCCGT
*
2676572 GTGCCAGGCC
131 GTGCCAGGCA
2676582 GTGTG
1 GTGTG
2676587 CTGGGCCGTG
Statistics
Matches: 139, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 139 1.00
ACGTcount: A:0.24, C:0.29, G:0.26, T:0.21
Consensus pattern (140 bp):
GTGTGACTCACACGGCCAAGAGACACACCTGTGTCTTAGGTCGTGTTGGTATTCAAAATAAGAGC
ACACGGCCGTGTCCCAGCCCGTGTAACTCACTGACTTGGGTCACAAGGCCAAACCACACGCCCGT
GTGCCAGGCA
Found at i:2678441 original size:25 final size:25
Alignment explanation
Indices: 2678362--2678434 Score: 119
Period size: 25 Copynumber: 2.9 Consensus size: 25
2678352 GCTATAAACG
*
2678362 GTAAGCTCTTTCGAGCTGAATAACA
1 GTAAGTTCTTTCGAGCTGAATAACA
2678387 GTAAGTTCTTTCGAGCTGAATAACA
1 GTAAGTTCTTTCGAGCTGAATAACA
* *
2678412 GTAAGTTTTTTCGAGTTGAATAA
1 GTAAGTTCTTTCGAGCTGAATAA
2678435 TGATAAGCTC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.34
Consensus pattern (25 bp):
GTAAGTTCTTTCGAGCTGAATAACA
Found at i:2679404 original size:29 final size:29
Alignment explanation
Indices: 2679371--2679536 Score: 140
Period size: 29 Copynumber: 5.7 Consensus size: 29
2679361 AAAAAAAATA
*
2679371 TAAATTACATTTTGGCCCCTAAACTTTTC
1 TAAATTACATTTTGACCCCTAAACTTTTC
**
2679400 TAAATTACATTTCAACCCCTAAACTTTTC
1 TAAATTACATTTTGACCCCTAAACTTTTC
** *
2679429 TAAATTACATTTCAACCCTTAAACTTTCTC
1 TAAATTACATTTTGACCCCTAAACTTT-TC
* * * *
2679459 AAAATTTCACTTTGACCCTTAAA-TTTTC
1 TAAATTACATTTTGACCCCTAAACTTTTC
* *
2679487 TAGGAATTACATTTTG-GCCCTATA-TTTTCC
1 TA--AATTACATTTTGACCCCTAAACTTTT-C
* *
2679517 TAAAATTGCATTTTTACCCC
1 T-AAATTACATTTTGACCCC
2679537 AAATGTTTTG
Statistics
Matches: 113, Mismatches: 18, Indels: 11
0.80 0.13 0.08
Matches are distributed among these distances:
28 3 0.03
29 74 0.65
30 35 0.31
31 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.05, T:0.41
Consensus pattern (29 bp):
TAAATTACATTTTGACCCCTAAACTTTTC
Found at i:2680100 original size:14 final size:13
Alignment explanation
Indices: 2680081--2680131 Score: 63
Period size: 12 Copynumber: 4.1 Consensus size: 13
2680071 AGATAAGGAG
2680081 AAGAGAAAGGAAAA
1 AAGAGAAA-GAAAA
2680095 AAGAGAAA-AAAA
1 AAGAGAAAGAAAA
*
2680107 AAGGGAAAG-AAA
1 AAGAGAAAGAAAA
2680119 AAGAG-AAGAAAA
1 AAGAGAAAGAAAA
2680131 A
1 A
2680132 GAAAAAAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 3 0.09
12 22 0.67
14 8 0.24
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (13 bp):
AAGAGAAAGAAAA
Found at i:2680106 original size:12 final size:12
Alignment explanation
Indices: 2680081--2680139 Score: 59
Period size: 12 Copynumber: 4.9 Consensus size: 12
2680071 AGATAAGGAG
2680081 AAGAGAAAGGAAAA
1 AAGAGAAA--AAAA
2680095 AAGAGAAAAAAA
1 AAGAGAAAAAAA
* *
2680107 AAGGGAAAGAAA
1 AAGAGAAAAAAA
*
2680119 AAGAG-AAGAAA
1 AAGAGAAAAAAA
2680130 AAGA-AAAAAA
1 AAGAGAAAAAA
2680140 CAAAAACAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
11 14 0.35
12 18 0.45
14 8 0.20
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAGAGAAAAAAA
Found at i:2681076 original size:17 final size:17
Alignment explanation
Indices: 2681045--2681346 Score: 158
Period size: 17 Copynumber: 17.4 Consensus size: 17
2681035 TTAAAAAAAG
*
2681045 AAAAAA-TTCGAGTTTC
1 AAAAAATTTCGTGTTTC
* *
2681061 AAAAAATGTCGTGTTTT
1 AAAAAATTTCGTGTTTC
*
2681078 AAAAATTTTCGTGTTTC
1 AAAAAATTTCGTGTTTC
* *
2681095 -TAAAATTTCCCTGTTT-
1 AAAAAATTT-CGTGTTTC
* * *
2681111 TAAAAATTCCCGTGTTTTTA
1 AAAAAATT-TCGTG--TTTC
*
2681131 AAAAAATGTCGTGTTTC
1 AAAAAATTTCGTGTTTC
*
2681148 AAAAATTTTCGTGTTTC
1 AAAAAATTTCGTGTTTC
*
2681165 AAAAATTTTCGTGTTT-
1 AAAAAATTTCGTGTTTC
* **
2681181 -ACAAATTCTCGTGTTAAAA
1 AAAAAATT-TCGTGTT--TC
2681200 AAAAACTTATTTCCGTGTTTC
1 AAAAA---ATTT-CGTGTTTC
* *
2681221 -TAAAATTTCCCTGTTT-
1 AAAAAATTT-CGTGTTTC
*
2681237 TAAAAATTCTCGTGTTTC
1 AAAAAATT-TCGTGTTTC
* *
2681255 AAAAAATGTCGTGTTTT
1 AAAAAATTTCGTGTTTC
2681272 AAAAAATTTCCGTGTTTC
1 AAAAAATTT-CGTGTTTC
* *
2681290 -TAAAATTTCCGTATTT-
1 AAAAAATTT-CGTGTTTC
*
2681306 TAAAAATTCTCGTGTTTTC
1 AAAAAATT-TCGTG-TTTC
2681325 -AAAAATTCTCGTGTTT-
1 AAAAAATT-TCGTGTTTC
2681341 AAAAAA
1 AAAAAA
2681347 ACTTTAGTTT
Statistics
Matches: 224, Mismatches: 37, Indels: 49
0.72 0.12 0.16
Matches are distributed among these distances:
15 5 0.02
16 19 0.08
17 140 0.62
18 31 0.14
19 7 0.03
20 12 0.05
22 1 0.00
23 9 0.04
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.42
Consensus pattern (17 bp):
AAAAAATTTCGTGTTTC
Found at i:2681146 original size:53 final size:52
Alignment explanation
Indices: 2681056--2681180 Score: 135
Period size: 53 Copynumber: 2.4 Consensus size: 52
2681046 AAAAATTCGA
* ** * * *
2681056 GTTTCAAAAAATGTCGTG-TTTTAAAAATTTTCGTGTTTCTAAAATTTCCCT
1 GTTTCAAAAATTCCCGTGTTTTTAAAAAATGTCGTGTTTCAAAAATTTCCCT
* * *
2681107 GTTTTAAAAATTCCCGTGTTTTTAAAAAAATGTCGTGTTTCAAAAATTTTCGT
1 GTTTCAAAAATTCCCGTGTTTTT-AAAAAATGTCGTGTTTCAAAAATTTCCCT
**
2681160 GTTTCAAAAATTTTCGTGTTT
1 GTTTCAAAAATTCCCGTGTTT
2681181 ACAAATTCTC
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
51 14 0.23
52 4 0.07
53 42 0.70
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.46
Consensus pattern (52 bp):
GTTTCAAAAATTCCCGTGTTTTTAAAAAATGTCGTGTTTCAAAAATTTCCCT
Found at i:2681239 original size:126 final size:126
Alignment explanation
Indices: 2681082--2681321 Score: 367
Period size: 126 Copynumber: 1.9 Consensus size: 126
2681072 TGTTTTAAAA
*
2681082 ATTTTCGTGTTTCTAAAATTTCCCTGTTTTAAAAATTCCCGTGTTTTTAAAAAAATGTCGTG-TT
1 ATTTCCGTGTTTCTAAAATTTCCCTGTTTTAAAAATTCCCGTG--TTTAAAAAAATGTCGTGTTT
* * * *
2681146 TCAAAAATTTTCGTGTTTCAAAAATTTTCGT-GTTTACAAATTCTCGTGTTAAAAAAAAACTT
64 TAAAAAATTTCCGTGTTTCAAAAATTTCCGTAGTTTAAAAATTCTCGTGTTAAAAAAAAACTT
* *
2681208 ATTTCCGTGTTTCTAAAATTTCCCTGTTTTAAAAATTCTCGTGTTTCAAAAAATGTCGTGTTTTA
1 ATTTCCGTGTTTCTAAAATTTCCCTGTTTTAAAAATTCCCGTGTTTAAAAAAATGTCGTGTTTTA
* *
2681273 AAAAATTTCCGTGTTTCTAAAATTTCCGTATTTTAAAAATTCTCGTGTT
66 AAAAATTTCCGTGTTTCAAAAATTTCCGTAGTTTAAAAATTCTCGTGTT
2681322 TTCAAAAATT
Statistics
Matches: 103, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
124 16 0.16
125 29 0.28
126 58 0.56
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (126 bp):
ATTTCCGTGTTTCTAAAATTTCCCTGTTTTAAAAATTCCCGTGTTTAAAAAAATGTCGTGTTTTA
AAAAATTTCCGTGTTTCAAAAATTTCCGTAGTTTAAAAATTCTCGTGTTAAAAAAAAACTT
Found at i:2681307 original size:69 final size:68
Alignment explanation
Indices: 2681056--2681347 Score: 284
Period size: 69 Copynumber: 4.2 Consensus size: 68
2681046 AAAAATTCGA
* * * * *
2681056 GTTTCAAAAAATGTCGTGTTT-TAAAAATTTTCGTGTTTCTAAAATTTC-CCTGTTTTAAAAATT
1 GTTTAAAAAAATGTCGTGTTTCT-AAAATTTCCGTGTTT-TAAAAATTCTCGTGTTTCAAAAATT
*
2681119 CCCGT
64 CTCGT
* * * * *
2681124 GTTTTTAAAAAAATGTCGTGTTTCAAAAATTTTCGTGTTTCAAAAATTTTCGTGTTT-ACAAATT
1 G--TTTAAAAAAATGTCGTGTTTCTAAAATTTCCGTGTTTTAAAAATTCTCGTGTTTCAAAAATT
2681188 CTCGT
64 CTCGT
* * *
2681193 GTTAAAAAAAAACTTATTTCCGTGTTTCTAAAATTTCCCTGTTTTAAAAATTCTCGTGTTTCAAA
1 GTT--TAAAAAA---ATGT-CGTGTTTCTAAAATTTCCGTGTTTTAAAAATTCTCGTGTTTCAAA
* *
2681258 AAATGTCGT
60 AATTCTCGT
* * *
2681267 GTTTTAAAAAATTTCCGTGTTTCTAAAATTTCCGTATTTTAAAAATTCTCGTGTTTTCAAAAATT
1 GTTTAAAAAAATGT-CGTGTTTCTAAAATTTCCGTGTTTTAAAAATTCTCGTG-TTTCAAAAATT
2681332 CTCGT
64 CTCGT
2681337 GTTTAAAAAAA
1 GTTTAAAAAAA
2681348 CTTTAGTTTT
Statistics
Matches: 187, Mismatches: 25, Indels: 22
0.80 0.11 0.09
Matches are distributed among these distances:
67 2 0.01
68 1 0.01
69 64 0.34
70 64 0.34
72 8 0.04
73 36 0.19
74 12 0.06
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.43
Consensus pattern (68 bp):
GTTTAAAAAAATGTCGTGTTTCTAAAATTTCCGTGTTTTAAAAATTCTCGTGTTTCAAAAATTCT
CGT
Found at i:2681342 original size:34 final size:33
Alignment explanation
Indices: 2681056--2681346 Score: 192
Period size: 34 Copynumber: 8.3 Consensus size: 33
2681046 AAAAATTCGA
* * *
2681056 GTTTCAAAAAATGTCGTGTTTTAAAAATTTTCGT
1 GTTT-AAAAAATTTCGTGTTTCAAAAATTCTCGT
** * * *
2681090 GTTTCTAAAATTTCCCTGTTTTAAAAATTCCCGT
1 GTTTAAAAAATTT-CGTGTTTCAAAAATTCTCGT
* *
2681124 GTTTTTAAAAAAATGTCGTGTTTCAAAAATTTTCGT
1 G--TTT-AAAAAATTTCGTGTTTCAAAAATTCTCGT
* *
2681160 GTTTCAAAAATTTTCGTGTTT-ACAAATTCTCGT
1 GTTT-AAAAAATTTCGTGTTTCAAAAATTCTCGT
* * *
2681193 GTTAAAAAAAAACTTATTTCCGTGTTTCTAAAATT-TCCCT
1 GTT---TAAAAA---ATTT-CGTGTTTCAAAAATTCT-CGT
* * *
2681233 GTTTTAAAAATTCTCGTGTTTCAAAAAATGTCGT
1 GTTTAAAAAATT-TCGTGTTTCAAAAATTCTCGT
*
2681267 GTTTTAAAAAATTTCCGTGTTTCTAAAATT-TCCGT
1 G-TTTAAAAAATTT-CGTGTTTCAAAAATTCT-CGT
* *
2681302 ATTTTAAAAATTCTCGTGTTTTCAAAAATTCTCGT
1 GTTTAAAAAATT-TCGTG-TTTCAAAAATTCTCGT
2681337 GTTTAAAAAA
1 GTTTAAAAAA
2681347 ACTTTAGTTT
Statistics
Matches: 200, Mismatches: 36, Indels: 41
0.72 0.13 0.15
Matches are distributed among these distances:
33 19 0.09
34 74 0.37
35 55 0.28
36 21 0.10
37 10 0.05
38 3 0.01
39 8 0.04
40 10 0.05
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.43
Consensus pattern (33 bp):
GTTTAAAAAATTTCGTGTTTCAAAAATTCTCGT
Found at i:2683855 original size:47 final size:47
Alignment explanation
Indices: 2683786--2683879 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
2683776 GGATTCTTCT
2683786 ATTTCTCCCTATAAATATGTGGCATTGGTAGAATTAAAAATACACAA
1 ATTTCTCCCTATAAATATGTGGCATTGGTAGAATTAAAAATACACAA
2683833 ATTTCTCCCTATAAATATGTGGCATTGGTAGAATTAAAAATACACAA
1 ATTTCTCCCTATAAATATGTGGCATTGGTAGAATTAAAAATACACAA
2683880 CTTTGAGATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (47 bp):
ATTTCTCCCTATAAATATGTGGCATTGGTAGAATTAAAAATACACAA
Found at i:2685528 original size:21 final size:21
Alignment explanation
Indices: 2685499--2685539 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2685489 GTTGGATGGA
2685499 AAAGAGAAAGAA-TGAAAGAAG
1 AAAGAGAAA-AAGTGAAAGAAG
*
2685520 AAAGTGAAAAAGTGAAAGAA
1 AAAGAGAAAAAGTGAAAGAA
2685540 AATAAATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.66, C:0.00, G:0.27, T:0.07
Consensus pattern (21 bp):
AAAGAGAAAAAGTGAAAGAAG
Found at i:2686006 original size:37 final size:36
Alignment explanation
Indices: 2685964--2686065 Score: 91
Period size: 37 Copynumber: 2.8 Consensus size: 36
2685954 AATATTATAA
2685964 TTAATATTCTTTTTATATTTTATAATTTTTAACAATT
1 TTAATATT-TTTTTATATTTTATAATTTTTAACAATT
**** * *
2686001 TTAATA-AAAATTATATGTTTTTAAATTTTTAATAATT
1 TTAATATTTTTTTATAT-TTTAT-AATTTTTAACAATT
*
2686038 TTAATATTTTTTGA-ATTTTCATAATTTT
1 TTAATATTTTTTTATATTTT-ATAATTTT
2686066 AATTTTTTAA
Statistics
Matches: 49, Mismatches: 12, Indels: 9
0.70 0.17 0.13
Matches are distributed among these distances:
35 6 0.12
36 13 0.27
37 28 0.57
38 2 0.04
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (36 bp):
TTAATATTTTTTTATATTTTATAATTTTTAACAATT
Found at i:2686039 original size:9 final size:9
Alignment explanation
Indices: 2686027--2686117 Score: 61
Period size: 9 Copynumber: 10.6 Consensus size: 9
2686017 GTTTTTAAAT
2686027 TTTTAATAA
1 TTTTAATAA
2686036 TTTTAAT-A
1 TTTTAATAA
*
2686044 TTTT-TTGAA
1 TTTTAAT-AA
*
2686053 TTTTCATAA
1 TTTTAATAA
*
2686062 TTTTAAT-T
1 TTTTAATAA
*
2686070 TTTTAAAAA
1 TTTTAATAA
2686079 TTTTAA-AA
1 TTTTAATAA
*
2686087 TATTGAAT--
1 T-TTTAATAA
2686095 TTTTAAATAA
1 TTTT-AATAA
2686105 TTTT-ATAA
1 TTTTAATAA
2686113 TTTTA
1 TTTTA
2686118 TTTAATTTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 20
0.70 0.09 0.22
Matches are distributed among these distances:
7 3 0.05
8 26 0.41
9 30 0.47
10 5 0.08
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.58
Consensus pattern (9 bp):
TTTTAATAA
Found at i:2686056 original size:26 final size:27
Alignment explanation
Indices: 2686013--2686117 Score: 87
Period size: 26 Copynumber: 4.0 Consensus size: 27
2686003 AATAAAAATT
2686013 ATATGTTTTTAAATTTTTAATAATTTTA
1 ATAT-TTTTTAAATTTTTAATAATTTTA
* *
2686041 ATATTTTTTGAA-TTTTCATAATTTTA
1 ATATTTTTTAAATTTTTAATAATTTTA
* * * *
2686067 AT-TTTTTAAAAATTTTAA-AATATTG
1 ATATTTTTTAAATTTTTAATAATTTTA
2686092 A-A-TTTTTAAATAATTTT-ATAATTTTA
1 ATATTTTTTAAAT--TTTTAATAATTTTA
2686118 TTTAATTTTT
Statistics
Matches: 61, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
24 7 0.11
25 14 0.23
26 29 0.48
27 7 0.11
28 4 0.07
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (27 bp):
ATATTTTTTAAATTTTTAATAATTTTA
Found at i:2686105 original size:43 final size:43
Alignment explanation
Indices: 2686019--2686116 Score: 110
Period size: 43 Copynumber: 2.3 Consensus size: 43
2686009 AATTATATGT
* * * *
2686019 TTTTAAATTTTTAATAATTTTAATATTTTTTGAATTTTCATAA
1 TTTTAAATTTTTAAAAATTTTAATATATATTGAATTTTAATAA
*
2686062 TTTTAATTTTTTAAAAATTTTAA-A-ATATTGAATTTTTAAATAA
1 TTTTAAATTTTTAAAAATTTTAATATATATTGAA-TTTT-AATAA
2686105 TTTTATAATTTT
1 TTTTA-AATTTT
2686117 ATTTAATTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
41 6 0.13
42 5 0.11
43 30 0.65
44 5 0.11
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (43 bp):
TTTTAAATTTTTAAAAATTTTAATATATATTGAATTTTAATAA
Found at i:2686156 original size:10 final size:8
Alignment explanation
Indices: 2686019--2686161 Score: 51
Period size: 8 Copynumber: 17.0 Consensus size: 8
2686009 AATTATATGT
*
2686019 TTTTAAAT
1 TTTTAAAA
2686027 TTTTAATAA
1 TTTTAA-AA
*
2686036 TTTTAATAT
1 TTTTAA-AA
**
2686045 TTTTTGAA
1 TTTTAAAA
*
2686053 TTTTCATAA
1 TTTT-AAAA
**
2686062 TTTTAATT
1 TTTTAAAA
2686070 TTTTAAAAA
1 TTTT-AAAA
2686079 TTTTAAAA
1 TTTTAAAA
* * *
2686087 TATTGAAT
1 TTTTAAAA
2686095 TTTTAAATAA
1 TTTT-AA-AA
*
2686105 TTTTATAA
1 TTTTAAAA
*
2686113 TTTTATTTAA
1 TTTTA--AAA
2686123 TTTT----
1 TTTTAAAA
2686127 TTTCTAAAA
1 TTT-TAAAA
2686136 TTTTAAAA
1 TTTTAAAA
2686144 TTTTAAATCA
1 TTTTAAA--A
2686154 TTTTAAAA
1 TTTTAAAA
2686162 GTTTCCTATA
Statistics
Matches: 102, Mismatches: 19, Indels: 28
0.68 0.13 0.19
Matches are distributed among these distances:
4 3 0.03
5 1 0.01
8 48 0.47
9 30 0.29
10 20 0.20
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.57
Consensus pattern (8 bp):
TTTTAAAA
Found at i:2688767 original size:17 final size:18
Alignment explanation
Indices: 2688747--2688782 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2688737 TTAAAAAAAA
2688747 TATAAAT-TTTAGAATTT
1 TATAAATATTTAGAATTT
2688764 TATAAATATTTAGAATTT
1 TATAAATATTTAGAATTT
2688782 T
1 T
2688783 TTTGTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
TATAAATATTTAGAATTT
Found at i:2688780 original size:26 final size:25
Alignment explanation
Indices: 2688716--2688782 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 25
2688706 GAAAAAAATT
2688716 AAAAT-TTTAAATTTCTAGAATTTAA
1 AAAATATTTAAATTT-TAGAATTTAA
* * *
2688741 AAAAAATATAAATTTTAGAATTTTA
1 AAAATATTTAAATTTTAGAATTTAA
*
2688766 TAAATATTTAGAATTTT
1 AAAATATTTA-AATTTT
2688783 TTTGTAATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
25 20 0.59
26 14 0.41
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (25 bp):
AAAATATTTAAATTTTAGAATTTAA
Found at i:2690201 original size:50 final size:50
Alignment explanation
Indices: 2690088--2690192 Score: 149
Period size: 49 Copynumber: 2.1 Consensus size: 50
2690078 ATTTTTTTTA
* * *
2690088 AATGAAAATAAATATTATTTTTTGGGTTTGCTTCAAAGTAAATATTATCT
1 AATGTAAATAAATATTATTTTTTGGATTTGCTTCAAAATAAATATTATCT
* *
2690138 AATGTAAATAAATATTA-TTTTTGGATTTGTTTTAAAATAAATATTATCT
1 AATGTAAATAAATATTATTTTTTGGATTTGCTTCAAAATAAATATTATCT
*
2690187 TATGTA
1 AATGTA
2690193 TTGAAAATAA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
49 33 0.67
50 16 0.33
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.47
Consensus pattern (50 bp):
AATGTAAATAAATATTATTTTTTGGATTTGCTTCAAAATAAATATTATCT
Found at i:2696243 original size:18 final size:17
Alignment explanation
Indices: 2696210--2696248 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
2696200 TTTTATAAAT
2696210 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
2696228 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
2696245 TGTG
1 TGTG
2696249 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:2702282 original size:28 final size:26
Alignment explanation
Indices: 2702251--2702315 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 26
2702241 ATAAAGATAT
*
2702251 TAAATATCAATAATAATTATGATTAAAA
1 TAAATAT-AATAATAATTA-GATGAAAA
* *
2702279 TAAAATATACTAATAATTAGATGAATA
1 T-AAATATAATAATAATTAGATGAAAA
2702306 TAAATATAAT
1 TAAATATAAT
2702316 TTATCTTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 8 0.25
27 7 0.22
28 11 0.34
29 6 0.19
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (26 bp):
TAAATATAATAATAATTAGATGAAAA
Found at i:2706685 original size:67 final size:67
Alignment explanation
Indices: 2706599--2706732 Score: 259
Period size: 67 Copynumber: 2.0 Consensus size: 67
2706589 AATGATTAAC
*
2706599 TATTGAATTGGTTATATAAGAACGTGATTTGGTGTTGTGTATGCTTAAATGATAGTTAATACAAA
1 TATTGAAGTGGTTATATAAGAACGTGATTTGGTGTTGTGTATGCTTAAATGATAGTTAATACAAA
2706664 GA
66 GA
2706666 TATTGAAGTGGTTATATAAGAACGTGATTTGGTGTTGTGTATGCTTAAATGATAGTTAATACAAA
1 TATTGAAGTGGTTATATAAGAACGTGATTTGGTGTTGTGTATGCTTAAATGATAGTTAATACAAA
2706731 GA
66 GA
2706733 AATTATAAAA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.38
Consensus pattern (67 bp):
TATTGAAGTGGTTATATAAGAACGTGATTTGGTGTTGTGTATGCTTAAATGATAGTTAATACAAA
GA
Found at i:2708124 original size:22 final size:24
Alignment explanation
Indices: 2708081--2708125 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 24
2708071 TAACTAAGCT
2708081 TACTTACTTTTCTAGCTTAATTTA
1 TACTTACTTTTCTAGCTTAATTTA
2708105 TACTT-CTTTTCTA-CTTAATTT
1 TACTTACTTTTCTAGCTTAATTT
2708126 CTTACCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.38
23 8 0.38
24 5 0.24
ACGTcount: A:0.22, C:0.18, G:0.02, T:0.58
Consensus pattern (24 bp):
TACTTACTTTTCTAGCTTAATTTA
Found at i:2708713 original size:5 final size:5
Alignment explanation
Indices: 2708694--2708768 Score: 59
Period size: 5 Copynumber: 15.4 Consensus size: 5
2708684 TTTGTTTGTT
* * * *
2708694 TAATA T-ATAA TAATA TAATA TAATA TAATA TATTA TATTA TATTA TATTA
1 TAATA TAAT-A TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
*
2708744 TATTA T-ATAA TAATA T-AT- TAATA TA
1 TAATA TAAT-A TAATA TAATA TAATA TA
2708769 TTTAAAAAAT
Statistics
Matches: 62, Mismatches: 2, Indels: 12
0.82 0.03 0.16
Matches are distributed among these distances:
3 1 0.02
4 7 0.11
5 50 0.81
6 4 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (5 bp):
TAATA
Found at i:2711834 original size:14 final size:15
Alignment explanation
Indices: 2711815--2711843 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2711805 TTAAGCTTAT
2711815 ATAAAAATA-TATAC
1 ATAAAAATAGTATAC
2711829 ATAAAAATAGTATAC
1 ATAAAAATAGTATAC
2711844 GATAGATCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.28
Consensus pattern (15 bp):
ATAAAAATAGTATAC
Found at i:2711939 original size:22 final size:22
Alignment explanation
Indices: 2711853--2711992 Score: 101
Period size: 24 Copynumber: 6.1 Consensus size: 22
2711843 CGATAGATCT
*
2711853 AAATAATGA-TATGATAAGTTTA
1 AAATAAT-ATTATGATAAATTTA
* *
2711875 AAATTACAGTA-CATGATAAATTTC
1 AAA-TA-A-TATTATGATAAATTTA
*
2711899 AAATTATGATGTATGATAAATTT-
1 AAATAAT-AT-TATGATAAATTTA
2711922 AAATAATATTAATGAT-AATTTA
1 AAATAATATT-ATGATAAATTTA
*
2711944 AAATAATAGTAT-ATTAAATATTA
1 AAATAATATTATGA-TAAAT-TTA
*
2711967 AAATAATACTAATGATAAATTTA
1 AAATAATA-TTATGATAAATTTA
2711990 AAA
1 AAA
2711993 CAATGTTAAG
Statistics
Matches: 96, Mismatches: 9, Indels: 25
0.74 0.07 0.19
Matches are distributed among these distances:
20 1 0.01
21 10 0.10
22 24 0.25
23 26 0.27
24 33 0.34
25 2 0.02
ACGTcount: A:0.52, C:0.03, G:0.08, T:0.37
Consensus pattern (22 bp):
AAATAATATTATGATAAATTTA
Found at i:2712017 original size:46 final size:44
Alignment explanation
Indices: 2711915--2712023 Score: 134
Period size: 46 Copynumber: 2.4 Consensus size: 44
2711905 TGATGTATGA
* *
2711915 TAAAT-TTAAATAATATTAATGATAATTTAAAATAATAGTATAT
1 TAAATATTAAATAATACTAATGATAATTTAAAACAATAGTATAT
2711958 TAAATATTAAAATAATACTAATGATAAATTTAAAACAAT-GT-TAAGCT
1 TAAATATT-AAATAATACTAATGAT-AATTTAAAACAATAGTAT-A--T
2712005 TAAATATTAAATAATACTA
1 TAAATATTAAATAATACTA
2712024 GATTTAAAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
43 5 0.09
44 3 0.05
45 18 0.31
46 23 0.40
47 9 0.16
ACGTcount: A:0.54, C:0.04, G:0.05, T:0.38
Consensus pattern (44 bp):
TAAATATTAAATAATACTAATGATAATTTAAAACAATAGTATAT
Found at i:2712906 original size:20 final size:19
Alignment explanation
Indices: 2712868--2712906 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2712858 AATTTTCAAA
**
2712868 TATTTTTAAAATATTTTTT
1 TATTTTTAAAATAAATTTT
*
2712887 TATTTTTAAAATAAAATTT
1 TATTTTTAAAATAAATTTT
2712906 T
1 T
2712907 GGTGTTTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTTTAAAATAAATTTT
Found at i:2712978 original size:35 final size:35
Alignment explanation
Indices: 2712925--2713001 Score: 127
Period size: 35 Copynumber: 2.2 Consensus size: 35
2712915 TTAAAAAAAT
*
2712925 GGGTCGTGCTGGGCCGGGCTTAGGAATATTTTCTC
1 GGGTCGGGCTGGGCCGGGCTTAGGAATATTTTCTC
* *
2712960 GGGTCGGGTTGGGTCGGGCTTAGGAATATTTTCTC
1 GGGTCGGGCTGGGCCGGGCTTAGGAATATTTTCTC
2712995 GGGTCGG
1 GGGTCGG
2713002 CTTAGACAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.10, C:0.17, G:0.42, T:0.31
Consensus pattern (35 bp):
GGGTCGGGCTGGGCCGGGCTTAGGAATATTTTCTC
Found at i:2713117 original size:19 final size:19
Alignment explanation
Indices: 2713093--2713148 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 19
2713083 GCCTGAACTC
2713093 GGCATTTTTAAATACTATT
1 GGCATTTTTAAATACTATT
*
2713112 GGCATTTCGTTTTTAATACTATT
1 GGCA--T--TTTTAAATACTATT
2713135 GGCATTTTTAAATA
1 GGCATTTTTAAATA
2713149 TTTTTATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
19 12 0.39
21 2 0.06
23 17 0.55
ACGTcount: A:0.29, C:0.11, G:0.12, T:0.48
Consensus pattern (19 bp):
GGCATTTTTAAATACTATT
Found at i:2713129 original size:23 final size:24
Alignment explanation
Indices: 2713097--2713141 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
2713087 GAACTCGGCA
2713097 TTTTTAAATACTATTGGCATTTCG
1 TTTTTAAATACTATTGGCATTTCG
2713121 TTTTT-AATACTATTGGCATTT
1 TTTTTAAATACTATTGGCATTT
2713142 TTAAATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.53
Consensus pattern (24 bp):
TTTTTAAATACTATTGGCATTTCG
Found at i:2713563 original size:102 final size:102
Alignment explanation
Indices: 2713445--2713651 Score: 398
Period size: 102 Copynumber: 2.0 Consensus size: 102
2713435 GGATCACGAT
2713445 TAAATATTAAATTGAACTTATATTTTTGAAAATTAAAGACAACGCA-GTTTAACGAGATACCAAT
1 TAAATATTAAATTGAACTTATATTTTTGAAAATT-AAGACAACGCACGTTTAACGAGATACCAAT
2713509 TTTGGGCGTCACGAGGGTGTTAATACCTTCTTTGTGCG
65 TTTGGGCGTCACGAGGGTGTTAATACCTTCTTTGTGCG
2713547 TAAATATTAAATTGAACTTATATTTTTGAAAATTAAGACAACGCACGTTTAACGAGATACCAATT
1 TAAATATTAAATTGAACTTATATTTTTGAAAATTAAGACAACGCACGTTTAACGAGATACCAATT
2713612 TTGGGCGTCACGAGGGTGTTAATACCTTCTTTGTGCG
66 TTGGGCGTCACGAGGGTGTTAATACCTTCTTTGTGCG
2713649 TAA
1 TAA
2713652 CCGACTCCTA
Statistics
Matches: 104, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
101 11 0.11
102 93 0.89
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.34
Consensus pattern (102 bp):
TAAATATTAAATTGAACTTATATTTTTGAAAATTAAGACAACGCACGTTTAACGAGATACCAATT
TTGGGCGTCACGAGGGTGTTAATACCTTCTTTGTGCG
Found at i:2714035 original size:16 final size:16
Alignment explanation
Indices: 2714010--2714059 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
2714000 TGGTTCGCTA
*
2714010 TATTGTATTAGAGGTG
1 TATTGAATTAGAGGTG
*
2714026 TATTGGATTAGAGGTG
1 TATTGAATTAGAGGTG
* *
2714042 TAATGAAATAGAGGTG
1 TATTGAATTAGAGGTG
2714058 TA
1 TA
2714060 ATAGCAAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (16 bp):
TATTGAATTAGAGGTG
Found at i:2714312 original size:16 final size:16
Alignment explanation
Indices: 2714275--2714316 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
2714265 TTAATCATAT
*
2714275 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
2714291 TT-AAATATATTATAA
1 TTAAAATATATTATAA
2714306 TTAAAATATAT
1 TTAAAATATAT
2714317 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:2714323 original size:14 final size:15
Alignment explanation
Indices: 2714284--2714325 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2714274 TTTAAACATA
*
2714284 ATTATTATTAAATAT
1 ATTATAATTAAATAT
2714299 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
2714313 A-TATAATTTAATA
1 ATTATAATTAAATA
2714326 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:2714537 original size:24 final size:25
Alignment explanation
Indices: 2714491--2714538 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
2714481 TATGAATTTG
2714491 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
2714517 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
2714539 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:2714542 original size:92 final size:92
Alignment explanation
Indices: 2714446--2714674 Score: 236
Period size: 92 Copynumber: 2.5 Consensus size: 92
2714436 TGATTTAATA
* * *
2714446 AAATTT-AAAATAATT-ATAACTAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TA
1 AAATTTCAAAA-AATTCATAA-TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTA
*
2714508 ATTATTACATATAATTTAATAATTAATATT
64 A-TATTAAATATAATTTAATAATTAATATT
* * * * *
2714538 AAATTTCATAAAATTCTTGATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAAT
1 AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
* *
2714603 ATTAAATATAATTTAAT-AGTGATA-T
66 ATTAAATATAATTTAATAATTAATATT
* * *
2714628 ATAATTTCATAAAATTCTTAATAATAAAATGT-TCTTATATGAATTTA
1 A-AATTTCAAAAAATTCATAATAAT-AAAT-TATATTATATGAATTTA
2714675 CTAAAATCAA
Statistics
Matches: 119, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
90 2 0.02
91 27 0.23
92 81 0.68
93 9 0.08
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (92 bp):
AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
ATTAAATATAATTTAATAATTAATATT
Found at i:2716307 original size:36 final size:36
Alignment explanation
Indices: 2716260--2716332 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
2716250 ACCCTTACAG
2716260 GATAGAACGATGGACTCCTAAGTATTCCCCATCTAA
1 GATAGAACGATGGACTCCTAAGTATTCCCCATCTAA
2716296 GATAGAACGATGGACTCCTAAGTATTCCCCATCTAA
1 GATAGAACGATGGACTCCTAAGTATTCCCCATCTAA
2716332 G
1 G
2716333 TTTTAATAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (36 bp):
GATAGAACGATGGACTCCTAAGTATTCCCCATCTAA
Found at i:2717596 original size:12 final size:12
Alignment explanation
Indices: 2717547--2717602 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
2717537 ATCACCCAAA
2717547 AAAGTATATATT
1 AAAGTATATATT
2717559 AAA-TGATAT-TT
1 AAAGT-ATATATT
* *
2717570 AAA-TACATTTT
1 AAAGTATATATT
2717581 AAAGTATATATT
1 AAAGTATATATT
2717593 AAAGGTATAT
1 AAA-GTATAT
2717603 GTAGTTTTGC
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
10 3 0.08
11 12 0.32
12 16 0.43
13 6 0.16
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (12 bp):
AAAGTATATATT
Found at i:2718275 original size:13 final size:13
Alignment explanation
Indices: 2718257--2718281 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2718247 AACTAATTTG
2718257 TATGTACTCTTTA
1 TATGTACTCTTTA
2718270 TATGTACTCTTT
1 TATGTACTCTTT
2718282 CACTAATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.16, G:0.08, T:0.56
Consensus pattern (13 bp):
TATGTACTCTTTA
Found at i:2720925 original size:22 final size:22
Alignment explanation
Indices: 2720887--2720935 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
2720877 AACTAGCACC
2720887 AAAAAATGAAACAAGCA-AAACG
1 AAAAAATGAAACAAGCAGAAA-G
*
2720909 AAAAAAT-AGAACGAGCAGAAAG
1 AAAAAATGA-AACAAGCAGAAAG
2720931 AAAAA
1 AAAAA
2720936 GAGTTAACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 1 0.04
22 20 0.83
23 3 0.12
ACGTcount: A:0.69, C:0.10, G:0.16, T:0.04
Consensus pattern (22 bp):
AAAAAATGAAACAAGCAGAAAG
Found at i:2721487 original size:22 final size:22
Alignment explanation
Indices: 2721449--2721497 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
2721439 AACTAGCACC
2721449 AAAAAATGAAACAAGCA-AAACG
1 AAAAAATGAAACAAGCAGAAA-G
*
2721471 AAAAAAT-AGAACGAGCAGAAAG
1 AAAAAATGA-AACAAGCAGAAAG
2721493 AAAAA
1 AAAAA
2721498 GAGTTAACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 1 0.04
22 20 0.83
23 3 0.12
ACGTcount: A:0.69, C:0.10, G:0.16, T:0.04
Consensus pattern (22 bp):
AAAAAATGAAACAAGCAGAAAG
Found at i:2724254 original size:20 final size:21
Alignment explanation
Indices: 2724229--2724270 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
2724219 TTAAAAAATA
2724229 AAATTCAA-ATTAAAATT-CTG
1 AAATTCAAGA-TAAAATTACTG
2724249 AAATTCAAGATAAAATTACTG
1 AAATTCAAGATAAAATTACTG
2724270 A
1 A
2724271 TATAGTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.31
Consensus pattern (21 bp):
AAATTCAAGATAAAATTACTG
Found at i:2726990 original size:23 final size:24
Alignment explanation
Indices: 2726948--2726995 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 24
2726938 TGAAAATAGG
2726948 CTCATTCAGCTTTAATTTC-ATTT
1 CTCATTCAGCTTTAATTTCAATTT
2726971 CTCATTCAGCTTCTAA-TTCAATTT
1 CTCATTCAGCTT-TAATTTCAATTT
2726995 C
1 C
2726996 CACCATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.23, C:0.25, G:0.04, T:0.48
Consensus pattern (24 bp):
CTCATTCAGCTTTAATTTCAATTT
Found at i:2727567 original size:46 final size:46
Alignment explanation
Indices: 2727500--2727638 Score: 242
Period size: 46 Copynumber: 3.0 Consensus size: 46
2727490 ATGCTATAAC
* *
2727500 TCAGTATGGTTTCCTTCACTGAAATACCATACCTACTTTTCACAAT
1 TCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAAT
*
2727546 TCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAAC
1 TCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAAT
*
2727592 CCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAAT
1 TCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAAT
2727638 T
1 T
2727639 TGCCATGGAT
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 87 1.00
ACGTcount: A:0.28, C:0.27, G:0.09, T:0.36
Consensus pattern (46 bp):
TCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAAT
Found at i:2729900 original size:19 final size:18
Alignment explanation
Indices: 2729876--2729920 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
2729866 GGTTTTCTCC
2729876 AAAATGAAAATGAAAATGA
1 AAAATGAAAATG-AAATGA
* **
2729895 AAAATGAATATGACCTGA
1 AAAATGAAAATGAAATGA
2729913 AAAATGAA
1 AAAATGAA
2729921 TTTATGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.62, C:0.04, G:0.16, T:0.18
Consensus pattern (18 bp):
AAAATGAAAATGAAATGA
Found at i:2733197 original size:13 final size:13
Alignment explanation
Indices: 2733179--2733203 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2733169 TAATTTATAT
2733179 GTGTGAAAATTTC
1 GTGTGAAAATTTC
2733192 GTGTGAAAATTT
1 GTGTGAAAATTT
2733204 TATCGTTGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:2734613 original size:41 final size:41
Alignment explanation
Indices: 2734576--2734705 Score: 215
Period size: 41 Copynumber: 3.2 Consensus size: 41
2734566 GACTATATGT
2734576 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
2734617 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
* * * * *
2734658 CTAGCAGGCTAAGTGCCAGTGAACTGAATTAGACTTTAAAC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
2734699 CTAGCAG
1 CTAGCAG
2734706 ATGAAGTGCT
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 84 1.00
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.21
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
Found at i:2734721 original size:41 final size:41
Alignment explanation
Indices: 2734548--2734705 Score: 208
Period size: 41 Copynumber: 3.9 Consensus size: 41
2734538 TCGGATTTAT
* * * * * *
2734548 TGCCAGTGAAATTATTCAGACTATATGTCTAGCAGGCTAAG
1 TGCCAGTGAACTGAATCAGGCTATAAGCCTAGCAGGCTAAG
*
2734589 TGCCGGTGAACTGAATCAGGCTATAAGCCTAGCAGGCTAAG
1 TGCCAGTGAACTGAATCAGGCTATAAGCCTAGCAGGCTAAG
*
2734630 TGCCGGTGAACTGAATCAGGCTATAAGCCTAGCAGGCTAAG
1 TGCCAGTGAACTGAATCAGGCTATAAGCCTAGCAGGCTAAG
* * * *
2734671 TGCCAGTGAACTGAATTAGACTTTAAACCTAGCAG
1 TGCCAGTGAACTGAATCAGGCTATAAGCCTAGCAG
2734706 ATGAAGTGCT
Statistics
Matches: 105, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 105 1.00
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.23
Consensus pattern (41 bp):
TGCCAGTGAACTGAATCAGGCTATAAGCCTAGCAGGCTAAG
Found at i:2745422 original size:23 final size:21
Alignment explanation
Indices: 2745393--2745444 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 21
2745383 TATTGATTCT
2745393 AAAAATTCAAAAA-AATTATAA
1 AAAAATTCAAAAAGAA-TATAA
2745414 ATAATAATTCAAAAAGAATATAA
1 A-AA-AATTCAAAAAGAATATAA
2745437 AAAAATTC
1 AAAAATTC
2745445 TAAGTTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 6 0.21
22 4 0.14
23 16 0.57
24 2 0.07
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.25
Consensus pattern (21 bp):
AAAAATTCAAAAAGAATATAA
Found at i:2750696 original size:2 final size:2
Alignment explanation
Indices: 2750689--2750857 Score: 320
Period size: 2 Copynumber: 84.5 Consensus size: 2
2750679 TATGAATAAA
2750689 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
2750731 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
2750773 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* *
2750815 AC AC AC AC AC AC AC AA AC AC AC AT AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
2750857 A
1 A
2750858 TTACAAAAGG
Statistics
Matches: 163, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 163 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.01
Consensus pattern (2 bp):
AC
Found at i:2751169 original size:13 final size:15
Alignment explanation
Indices: 2751150--2751183 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
2751140 CAGAAAGAAA
*
2751150 AAAAAAAGATA-ACC
1 AAAAAAAGAAACACC
2751164 AAAAAAAGAAACACC
1 AAAAAAAGAAACACC
2751179 AAAAA
1 AAAAA
2751184 TTTCAGCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.76, C:0.15, G:0.06, T:0.03
Consensus pattern (15 bp):
AAAAAAAGAAACACC
Found at i:2759106 original size:3 final size:3
Alignment explanation
Indices: 2759098--2759125 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2759088 TGACTGAGTC
2759098 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2759126 TGAATCAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2761674 original size:17 final size:17
Alignment explanation
Indices: 2761648--2761681 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2761638 AAAAAACAAC
2761648 CCTTTCTTTTTCCTTTT
1 CCTTTCTTTTTCCTTTT
* *
2761665 CCTTTTTTTTTTCTTTT
1 CCTTTCTTTTTCCTTTT
2761682 TTTACCTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (17 bp):
CCTTTCTTTTTCCTTTT
Found at i:2763557 original size:13 final size:13
Alignment explanation
Indices: 2763539--2763564 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2763529 TGAATATAAC
2763539 ATTATTGGGAGTG
1 ATTATTGGGAGTG
2763552 ATTATTGGGAGTG
1 ATTATTGGGAGTG
2763565 GCATCCACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.38, T:0.38
Consensus pattern (13 bp):
ATTATTGGGAGTG
Found at i:2770752 original size:31 final size:29
Alignment explanation
Indices: 2770682--2770755 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
2770672 GACTCAAGTT
* *
2770682 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTCAAATGTA
* **
2770711 ACGTTTTAGTCACTTATGTTATCATGTTGTA
1 ACATTTTAGTCACTTATGTT-TCA-AATGTA
2770742 ACATTTTAGTCACT
1 ACATTTTAGTCACT
2770756 GAGCCGTTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 19 0.51
30 2 0.05
31 16 0.43
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.47
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTCAAATGTA
Found at i:2771375 original size:31 final size:29
Alignment explanation
Indices: 2771311--2771379 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
2771301 ACGATAACGT
* *
2771311 AAGTGACTAAAACGTAACATTTCAAACAT
1 AAGTGACTAAAACGTAACATGTCAAACAA
* *
2771340 AAGTGACTAAAATGTAACCTGAGTCAAACAA
1 AAGTGACTAAAACGTAACAT--GTCAAACAA
2771371 AAGTGACTA
1 AAGTGACTA
2771380 TTTTGATAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.53
31 16 0.47
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.22
Consensus pattern (29 bp):
AAGTGACTAAAACGTAACATGTCAAACAA
Found at i:2775490 original size:21 final size:21
Alignment explanation
Indices: 2775466--2775505 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2775456 ATGTAAATCT
* *
2775466 TAAAAGTAAATAGACTAAAAA
1 TAAAAATAAAAAGACTAAAAA
2775487 TAAAAATAAAAAGACTAAA
1 TAAAAATAAAAAGACTAAA
2775506 TTTCGAACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.70, C:0.05, G:0.07, T:0.17
Consensus pattern (21 bp):
TAAAAATAAAAAGACTAAAAA
Found at i:2790418 original size:21 final size:21
Alignment explanation
Indices: 2790384--2790459 Score: 80
Period size: 21 Copynumber: 3.4 Consensus size: 21
2790374 TGAAGTCTTC
2790384 CTTAGAAGGTGGATATCGCGATA
1 CTTA-AAGG-GGATATCGCGATA
2790407 CTTAAAGGGGATATCGCGATA
1 CTTAAAGGGGATATCGCGATA
** * *
2790428 CCAAAAGGGGATACCGTGATA
1 CTTAAAGGGGATATCGCGATA
2790449 CTACTAAAGGG
1 CT--TAAAGGG
2790460 AATCCTTTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
21 31 0.69
22 4 0.09
23 10 0.22
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.21
Consensus pattern (21 bp):
CTTAAAGGGGATATCGCGATA
Found at i:2791023 original size:15 final size:16
Alignment explanation
Indices: 2790998--2791027 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2790988 ACAAATTGAA
2790998 AATACATTAAAATAGC
1 AATACATTAAAATAGC
2791014 AATA-ATTAAAATAG
1 AATACATTAAAATAG
2791028 TAGCAACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.27
Consensus pattern (16 bp):
AATACATTAAAATAGC
Found at i:2791078 original size:44 final size:44
Alignment explanation
Indices: 2791020--2791103 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 44
2791010 TAGCAATAAT
*
2791020 TAAAATAGTAGCAACTTAACAAGTAAATGCCTCTTAAATAACAC
1 TAAAATAGTAGCAACTTAACAAGTAAATGCCTCTAAAATAACAC
* * * *
2791064 TAAAGTAGTTGCAACTTAGCAATTAAATGCCTCTAAAATA
1 TAAAATAGTAGCAACTTAACAAGTAAATGCCTCTAAAATA
2791104 GTAGCTAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.27
Consensus pattern (44 bp):
TAAAATAGTAGCAACTTAACAAGTAAATGCCTCTAAAATAACAC
Found at i:2795379 original size:11 final size:10
Alignment explanation
Indices: 2795344--2795370 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2795334 CTAAGATGAT
2795344 TGTTTTGGCA
1 TGTTTTGGCA
2795354 TGTTTTGGCA
1 TGTTTTGGCA
2795364 TGTTTTG
1 TGTTTTG
2795371 AGTATGTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.07, C:0.07, G:0.30, T:0.56
Consensus pattern (10 bp):
TGTTTTGGCA
Found at i:2795769 original size:42 final size:42
Alignment explanation
Indices: 2795679--2795759 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
2795669 CACGAGCTGG
* *
2795679 GACACGACTGTGTGTCTCTAGTTCGAATGTTACACGGGCAAC
1 GACACGACTGTGTGTCCCTAGTTCGAATGTTACACGGCCAAC
* *
2795721 GACACGACTGTGTGTCCCTATTTCGATTGTTACACGGCC
1 GACACGACTGTGTGTCCCTAGTTCGAATGTTACACGGCC
2795760 TGAGACACGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.21, C:0.26, G:0.25, T:0.28
Consensus pattern (42 bp):
GACACGACTGTGTGTCCCTAGTTCGAATGTTACACGGCCAAC
Found at i:2809825 original size:21 final size:20
Alignment explanation
Indices: 2809796--2809834 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2809786 TAAACATTGA
2809796 AACCCTTAAAAACCTAACCCC
1 AACCCTT-AAAACCTAACCCC
* *
2809817 AACCTTTAAACCCTAACC
1 AACCCTTAAAACCTAACC
2809835 ATTAACCCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.41, C:0.41, G:0.00, T:0.18
Consensus pattern (20 bp):
AACCCTTAAAACCTAACCCC
Found at i:2810169 original size:7 final size:7
Alignment explanation
Indices: 2810157--2810198 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
2810147 CAATTTTAGT
2810157 TTTATGG
1 TTTATGG
*
2810164 TTTATGA
1 TTTATGG
2810171 TTTATGG
1 TTTATGG
2810178 TTTATGG
1 TTTATGG
2810185 -TTA-GAG
1 TTTATG-G
2810191 TTTATGG
1 TTTATGG
2810198 T
1 T
2810199 CTAAAGTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
5 1 0.03
6 4 0.13
7 24 0.80
8 1 0.03
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.55
Consensus pattern (7 bp):
TTTATGG
Found at i:2810288 original size:7 final size:7
Alignment explanation
Indices: 2810257--2810323 Score: 64
Period size: 7 Copynumber: 9.7 Consensus size: 7
2810247 TAGGGCTTCA
2810257 AGTTTTG
1 AGTTTTG
2810264 -GTTTTG
1 AGTTTTG
* *
2810270 AATTTGG
1 AGTTTTG
2810277 AGTTTTG
1 AGTTTTG
*
2810284 AGTTTAG
1 AGTTTTG
*
2810291 GGTTTTG
1 AGTTTTG
**
2810298 AGTTTCA
1 AGTTTTG
*
2810305 ATTTTTG
1 AGTTTTG
2810312 AGTTTTG
1 AGTTTTG
2810319 AGTTT
1 AGTTT
2810324 CAGATTTATG
Statistics
Matches: 45, Mismatches: 14, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
6 6 0.13
7 39 0.87
ACGTcount: A:0.16, C:0.01, G:0.27, T:0.55
Consensus pattern (7 bp):
AGTTTTG
Found at i:2810296 original size:28 final size:28
Alignment explanation
Indices: 2810263--2810316 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
2810253 TTCAAGTTTT
**
2810263 GGTTTTGAATTTGGAGTTTTGAGTTTAG
1 GGTTTTGAATTTCAAGTTTTGAGTTTAG
* *
2810291 GGTTTTGAGTTTCAATTTTTGAGTTT
1 GGTTTTGAATTTCAAGTTTTGAGTTT
2810317 TGAGTTTCAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.17, C:0.02, G:0.28, T:0.54
Consensus pattern (28 bp):
GGTTTTGAATTTCAAGTTTTGAGTTTAG
Found at i:2810300 original size:21 final size:21
Alignment explanation
Indices: 2810219--2810302 Score: 55
Period size: 21 Copynumber: 4.0 Consensus size: 21
2810209 GGGTTTTTGG
* *
2810219 TTGATTTTAGGGTTTT-AGGT
1 TTGAGTTTAGGGTTTTGAGTT
* * **
2810239 TTAAGGTTTAGGGCTTCAAGTT
1 TTGA-GTTTAGGGTTTTGAGTT
* ** *
2810261 TTG-GTTTTGAATTTGGAGTT
1 TTGAGTTTAGGGTTTTGAGTT
2810281 TTGAGTTTAGGGTTTTGAGTT
1 TTGAGTTTAGGGTTTTGAGTT
2810302 T
1 T
2810303 CAATTTTTGA
Statistics
Matches: 45, Mismatches: 16, Indels: 5
0.68 0.24 0.08
Matches are distributed among these distances:
20 17 0.38
21 23 0.51
22 5 0.11
ACGTcount: A:0.17, C:0.02, G:0.30, T:0.51
Consensus pattern (21 bp):
TTGAGTTTAGGGTTTTGAGTT
Found at i:2810337 original size:21 final size:20
Alignment explanation
Indices: 2810286--2810337 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
2810276 GAGTTTTGAG
*
2810286 TTTAGGGTTTTGAGTTTCAA
1 TTTATGGTTTTGAGTTTCAA
*
2810306 TTTTTGAGTTTTGAGTTTCAGA
1 TTTATG-GTTTTGAGTTTCA-A
2810328 TTTATGGTTT
1 TTTATGGTTT
2810338 AAGGTACAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.15
21 17 0.63
22 6 0.22
ACGTcount: A:0.17, C:0.04, G:0.23, T:0.56
Consensus pattern (20 bp):
TTTATGGTTTTGAGTTTCAA
Found at i:2816086 original size:19 final size:19
Alignment explanation
Indices: 2816055--2816092 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
2816045 TTTTAAAAAC
2816055 AATTTAACTTTGATTGAAA
1 AATTTAACTTTGATTGAAA
2816074 AATTCTAAC-TTGATTGAAA
1 AATT-TAACTTTGATTGAAA
2816093 CTATTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (19 bp):
AATTTAACTTTGATTGAAA
Found at i:2816108 original size:20 final size:19
Alignment explanation
Indices: 2816057--2816108 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
2816047 TTAAAAACAA
2816057 TTTAACTTTGATTGAAAAAT
1 TTTAA-TTTGATTGAAAAAT
* * *
2816077 TCTAACTTGATTGAAACTAT
1 TTTAATTTGATTGAAA-AAT
2816097 TTTAATTTGATT
1 TTTAATTTGATT
2816109 TAAAGGTTGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.48
Consensus pattern (19 bp):
TTTAATTTGATTGAAAAAT
Found at i:2816143 original size:13 final size:13
Alignment explanation
Indices: 2816127--2816152 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2816117 GATTCAAAAG
2816127 TTTTCTAAGAGTT
1 TTTTCTAAGAGTT
2816140 TTTTCTAAGAGTT
1 TTTTCTAAGAGTT
2816153 CAAAGTAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (13 bp):
TTTTCTAAGAGTT
Found at i:2816811 original size:7 final size:7
Alignment explanation
Indices: 2816799--2816844 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
2816789 TCAAAAATTA
2816799 TAAAAAT
1 TAAAAAT
2816806 TAAAAAT
1 TAAAAAT
*
2816813 TAAAAAA
1 TAAAAAT
*
2816820 T-CAAAT
1 TAAAAAT
2816826 T-AAAAT
1 TAAAAAT
*
2816832 TAAAAAA
1 TAAAAAT
2816839 TAAAAA
1 TAAAAA
2816845 GTTCATAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
6 9 0.27
7 24 0.73
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (7 bp):
TAAAAAT
Found at i:2816812 original size:16 final size:16
Alignment explanation
Indices: 2816786--2816824 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
2816776 GTTAACAAAT
2816786 AATTCAAAAATTATAAA
1 AATTCAAAAATTA-AAA
2816803 AATT-AAAAATTAAAA
1 AATTCAAAAATTAAAA
2816818 AA-TCAAA
1 AATTCAAA
2816825 TTAAAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 1 0.05
15 8 0.38
16 8 0.38
17 4 0.19
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (16 bp):
AATTCAAAAATTAAAA
Found at i:2816832 original size:19 final size:20
Alignment explanation
Indices: 2816802--2816839 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
2816792 AAAATTATAA
2816802 AAATTAAAAATTAAAAAATC
1 AAATTAAAAATTAAAAAATC
2816822 AAATT-AAAATTAAAAAAT
1 AAATTAAAAATTAAAAAAT
2816840 AAAAAGTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
AAATTAAAAATTAAAAAATC
Found at i:2816842 original size:13 final size:15
Alignment explanation
Indices: 2816786--2816844 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 15
2816776 GTTAACAAAT
2816786 AATTCAAAAATTATAAA
1 AATT-AAAAATTA-AAA
2816803 AATTAAAAATTAAAA
1 AATTAAAAATTAAAA
*
2816818 AA-T-CAAATT--AA
1 AATTAAAAATTAAAA
*
2816829 AATTAAAAAATAAAA
1 AATTAAAAATTAAAA
2816844 A
1 A
2816845 GTTCATAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
11 4 0.11
12 1 0.03
13 9 0.26
14 1 0.03
15 8 0.23
16 8 0.23
17 4 0.11
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.25
Consensus pattern (15 bp):
AATTAAAAATTAAAA
Found at i:2823635 original size:2 final size:2
Alignment explanation
Indices: 2823630--2823654 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2823620 AAAATAAAAA
2823630 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
2823655 GAGGGAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2845922 original size:18 final size:18
Alignment explanation
Indices: 2845899--2845935 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2845889 ATAATTAAAG
2845899 TTAAAA-TATTTTTTATTT
1 TTAAAATTA-TTTTTATTT
2845917 TTAAAATTATTTTTATTT
1 TTAAAATTATTTTTATTT
2845935 T
1 T
2845936 ATATAAGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTAAAATTATTTTTATTT
Found at i:2846935 original size:111 final size:112
Alignment explanation
Indices: 2846786--2846988 Score: 313
Period size: 111 Copynumber: 1.8 Consensus size: 112
2846776 ACACATTGAA
*
2846786 AAAAAAAATTTTGGTGTTGGCCAGTAGATGGTCAGCACCAAGTACATTTTTCGGGTCCCAAGGCA
1 AAAAAAAATTTTGGTGCTGGCCAGTAGATGGTCAGCACCAAGTACATTTTTCGGGTCCCAAGGCA
2846851 A-TTTTTTTTACTTTGGGACACTGATCGCCGACACCAATGTCAATTT
66 ATTTTTTTTTACTTTGGGACACTGATCGCCGACACCAATGTCAATTT
* * *
2846897 AAAAAAAA-TTTGAGTGCTGGTCAGTAGATGG-CTGGCACCAGGTACATTTTTCGGGTCCCAAGG
1 AAAAAAAATTTTG-GTGCTGGCCAGTAGATGGTC-AGCACCAAGTACATTTTTCGGGTCCCAAGG
*
2846960 TAATTTTTTTTTTACTTTGGGACACTGAT
64 CAA-TTTTTTTTTACTTTGGGACACTGAT
2846989 GGACGGCACC
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
110 5 0.06
111 54 0.65
113 24 0.29
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (112 bp):
AAAAAAAATTTTGGTGCTGGCCAGTAGATGGTCAGCACCAAGTACATTTTTCGGGTCCCAAGGCA
ATTTTTTTTTACTTTGGGACACTGATCGCCGACACCAATGTCAATTT
Found at i:2851773 original size:46 final size:46
Alignment explanation
Indices: 2851701--2851811 Score: 168
Period size: 46 Copynumber: 2.4 Consensus size: 46
2851691 NNNNNNNNNN
* * *
2851701 AAGAAAACCATACTGAGTTGTTAAAAGTAGGTATGGTGTTTAGGTA
1 AAGAAAACCATACTGAGTTGTGAAAAGTAGGTATGGTATTTACGTA
* * *
2851747 AAGAAAACTATACTGAGTTGTGAAAAGTAGGTATGGTATTTCCGTG
1 AAGAAAACCATACTGAGTTGTGAAAAGTAGGTATGGTATTTACGTA
2851793 AAGAAAACCATACTGAGTT
1 AAGAAAACCATACTGAGTT
2851812 ATAGCAATGT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 58 1.00
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29
Consensus pattern (46 bp):
AAGAAAACCATACTGAGTTGTGAAAAGTAGGTATGGTATTTACGTA
Found at i:2853257 original size:44 final size:44
Alignment explanation
Indices: 2853210--2853402 Score: 350
Period size: 44 Copynumber: 4.4 Consensus size: 44
2853200 TTATTCCTAA
* * *
2853210 TTTAAAACACGTTAAATTATAATACAATATACATGCATATTTAA
1 TTTAAAACACATTAAATTATAATACAATATACATACATATTTAT
*
2853254 TTTAAAGCACATTAAATTATAATACAATATACATACATATTTAT
1 TTTAAAACACATTAAATTATAATACAATATACATACATATTTAT
2853298 TTTAAAACACATTAAATTATAATACAATATACATACATATTTAT
1 TTTAAAACACATTAAATTATAATACAATATACATACATATTTAT
2853342 TTTAAAACACATTAAATTATAATACAATATACATACATATTTAT
1 TTTAAAACACATTAAATTATAATACAATATACATACATATTTAT
2853386 TTTAAAACACATTAAAT
1 TTTAAAACACATTAAAT
2853403 GAAAAATAAA
Statistics
Matches: 144, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 144 1.00
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (44 bp):
TTTAAAACACATTAAATTATAATACAATATACATACATATTTAT
Found at i:2853496 original size:48 final size:48
Alignment explanation
Indices: 2853444--2854155 Score: 1358
Period size: 48 Copynumber: 14.9 Consensus size: 48
2853434 ATAAAAAGCG
* * *
2853444 TAAATTAAAATGGAAAGAAAGATAATTTAAATGAAATGAGAAAAAAAT
1 TAAATTTAAATGAAAAAAAAGATAATTTAAATGAAATGAGAAAAAAAT
2853492 TAAATTTAAATGAAAAAAAAGATAATTTAAATGAAATGAGAAAAAAAT
1 TAAATTTAAATGAAAAAAAAGATAATTTAAATGAAATGAGAAAAAAAT
2853540 TAAATTTAAATGAAAAAAAAGATAATTTAAATGAAATGAGAAAAAAAT
1 TAAATTTAAATGAAAAAAAAGATAATTTAAATGAAATGAGAAAAAAAT
2853588 TAAATTTAAATGAAAAAAAAGATAATTTAAATGAAATGAGAAAAAAAT
1 TAAATTTAAATGAAAAAAAAGATAATTTAAATGAAATGAGAAAAAAAT
2853636 TAAATTTAAATGAAAAAAAAGATAATTTAAATGAAATGAGAAAAAAAT
1 TAAATTTAAATGAAAAAAAAGATAATTTAAATGAAATGAGAAAAAAAT
2853684 TAAATTTAAATGAAAAAAAAGATAATTTAAATGAAATGAGAAAAAAAT
1 TAAATTTAAATGAAAAAAAAGATAATTTAAATGAAATGAGAAAAAAAT
2853732 TAAATTTAAATGAAAAAAAAGATAATTTAAATGAAATGAGAAAAAAAT
1 TAAATTTAAATGAAAAAAAAGATAATTTAAATGAAATGAGAAAAAAAT
2853780 TAAATTTAAATGAAAAAAAAGATAATTTAAATGAAATGAGAAAAAAAT
1 TAAATTTAAATGAAAAAAAAGATAATTTAAATGAAATGAGAAAAAAAT
2853828 TAAATTTAAATGAAAAAAAAGATAATTTAAATGAAATGAGAAAAAAAT
1 TAAATTTAAATGAAAAAAAAGATAATTTAAATGAAATGAGAAAAAAAT
2853876 TAAATTTAAATGAAAAAAAAGATAATTTAAATGAAATGAGAAAAAAAT
1 TAAATTTAAATGAAAAAAAAGATAATTTAAATGAAATGAGAAAAAAAT
2853924 TAAATTTAAATGAAAAAAAAGATAATTTAAATGAAATGAGAAAAAAAT
1 TAAATTTAAATGAAAAAAAAGATAATTTAAATGAAATGAGAAAAAAAT
2853972 TAAATTTAAATGAAAAAAAAGATAATTTAAATGAAATGAGAAAAAAAT
1 TAAATTTAAATGAAAAAAAAGATAATTTAAATGAAATGAGAAAAAAAT
2854020 TAAATTTAAATGAAAAAAAAGATAATTTAAATGAAATGAGAAAAAAAT
1 TAAATTTAAATGAAAAAAAAGATAATTTAAATGAAATGAGAAAAAAAT
2854068 TAAATTTAAATGAAAAAAAAGATAATTTAAATGAAATGAG-AAAAAAT
1 TAAATTTAAATGAAAAAAAAGATAATTTAAATGAAATGAGAAAAAAAT
* *
2854115 TAAATTTAAATG-AAAAAAAGGTAATTTAAATAAAAT-AGAAA
1 TAAATTTAAATGAAAAAAAAGATAATTTAAATGAAATGAGAAA
2854156 TAGAAATGAA
Statistics
Matches: 658, Mismatches: 5, Indels: 4
0.99 0.01 0.01
Matches are distributed among these distances:
45 2 0.00
46 24 0.04
47 19 0.03
48 613 0.93
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.25
Consensus pattern (48 bp):
TAAATTTAAATGAAAAAAAAGATAATTTAAATGAAATGAGAAAAAAAT
Found at i:2854166 original size:5 final size:5
Alignment explanation
Indices: 2854142--2854242 Score: 69
Period size: 5 Copynumber: 18.6 Consensus size: 5
2854132 AAGGTAATTT
* * * *
2854142 AAATA AAATAG AAATAG AAATG AAATAC AAATAC AAATT AAATG AAATG
1 AAATG AAAT-G AAAT-G AAATG AAAT-G AAAT-G AAATG AAATG AAATG
*
2854191 AAATG AAAAT- ACATATG AAATA AAATG AAATAG AAATAG AAATG AAATG
1 AAATG -AAATG A-A-ATG AAATG AAATG AAAT-G AAAT-G AAATG AAATG
2854240 AAA
1 AAA
2854243 AAAAAAAGAT
Statistics
Matches: 83, Mismatches: 6, Indels: 14
0.81 0.06 0.14
Matches are distributed among these distances:
4 1 0.01
5 43 0.52
6 38 0.46
7 1 0.01
ACGTcount: A:0.65, C:0.03, G:0.12, T:0.20
Consensus pattern (5 bp):
AAATG
Found at i:2854167 original size:22 final size:21
Alignment explanation
Indices: 2854142--2854242 Score: 96
Period size: 22 Copynumber: 4.6 Consensus size: 21
2854132 AAGGTAATTT
2854142 AAATAAAATAGAAATAGAAATG
1 AAATAAAAT-GAAATAGAAATG
* *
2854164 AAATACAAATACAAAT-TAAATG
1 AAATA-AAAT-GAAATAGAAATG
* * *
2854186 AAATGAAATGAAAATACATATG
1 AAATAAAATG-AAATAGAAATG
2854208 AAATAAAATGAAATAGAAATAG
1 AAATAAAATGAAATAGAAAT-G
*
2854230 AAATGAAATGAAA
1 AAATAAAATGAAA
2854243 AAAAAAAGAT
Statistics
Matches: 65, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
21 16 0.25
22 40 0.62
23 9 0.14
ACGTcount: A:0.65, C:0.03, G:0.12, T:0.20
Consensus pattern (21 bp):
AAATAAAATGAAATAGAAATG
Done.